@ARTICLE{Akker99, author = {F. van den Akker and W. G. Hol}, title = {Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 1)}, pages = {206-18}, month = {January}, abstract = {Methods for the evaluation of the accuracy of crystal structures of proteins and nucleic acids are of general importance for structure-function studies as well as for biotechnological and biomedical research based upon three-dimensional structures of biomacromolecules. The structure-validation program DDQ (difference-density quality) has been developed to complement existing validation procedures. The DDQ method is based on the information present in a difference electron-density map calculated with the water molecules deliberately omitted from the structure-factor calculation. The quality of a crystal structure is reflected in this difference map by (i) the height of solvent peaks occurring at physical chemically reasonable positions with respect to protein and ligand atoms and (ii) the number and height of positive and negative 'shift' peaks next to protein atoms. The higher the solvent peaks and the lower the shift peaks, the better the structure is likely to be. Moreover, extraneous positive density due to an incomplete molecular model is also monitored, since this is another indicator of imperfections in the structure. Automated analysis of these types of features in difference electron densities is used to quantify the local as well as global accuracy of a structure. In the case of proteins, the DDQ structure-validation method is found to be very sensitive to small local errors, to omitted atoms and also to global errors in crystal structure determinations.}, keywords = {*Crystallography, X-Ray Electrochemistry Macromolecular Systems Models, Molecular Nucleic Acids/*chemistry Protein Conformation Proteins/*chemistry *Software Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.}, affiliation = {Department of Biochemistry, University of Washington, Seattle, WA 98195-7420, USA.}, } @ARTICLE{Badger97, author = {J. Badger}, title = {Modeling and refinement of water molecules and disordered solvent}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {344-52}, } @ARTICLE{Bernard94, author = {Y. Bernard and S. Degoy and F. Lefaucheux and M. C. Robert}, title = {A gel-mediated feeding technique for protein crystal growth from hanging drops}, journal = {Acta Cryst D}, year = {1994}, volume = {50}, pages = {504-7}, } @ARTICLE{Boggon00, author = {T. J. Boggon and L. Shapiro}, title = {Screening for phasing atoms in protein crystallography.}, journal = {Structure Fold Des}, year = {2000}, volume = {8}, number = {7}, pages = {R143-9}, month = {Jul 15}, keywords = {Binding Sites Bromine/analysis Color Crystallization Crystallography, X-Ray/*methods Iodine/analysis Metals, Rare Earth/analysis *Protein Conformation Scattering, Radiation Selenium/analysis Selenomethionine/chemistry Support, Non-U.S. Gov't}, affiliation = {Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA.}, } @ARTICLE{Bolotovsky98, author = {R. Bolotovsky and I. Steller and M. G. Rossmann}, title = {The use of partial reflections for scaling and averaging X-ray area-detector data}, journal = {J Appl Cryst}, year = {1998}, volume = {31}, pages = {708-17}, } @ARTICLE{Bourgeois99, author = {D. Bourgeois}, title = {New processing tools for weak and/or spatially overlapped macromolecular diffraction patterns.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1733-41}, month = {October}, abstract = {Tools originally developed for the treatment of weak and/or spatially overlapped time-resolved Laue patterns were extended to improve the processing of difficult monochromatic data sets. The integration program PrOW allows deconvolution of spatially overlapped spots which are usually rejected by standard packages. By using dynamically adjusted profile-fitting areas, a carefully built library of reference spots and interpolation of reference profiles, this program also provides a more accurate evaluation of weak spots. In addition, by using Wilson statistics, it allows rejection of non-redundant strong outliers such as zingers, which otherwise may badly corrupt the data. A weighting method for optimizing structure-factor amplitude differences, based on Bayesian statistics and originally applied to low signal-to-noise ratio time-resolved Laue data, is also shown to significantly improve other types of subtle amplitude differences, such as anomalous differences.}, keywords = {Computer Graphics Crystallography, X-Ray/*methods Fourier Analysis Proteins/*chemistry Software Synchrotrons Transferases/chemistry}, affiliation = {ESRF, BP 220, 38043 Grenoble CEDEX, France and LCCP, UPR 9015, IBS, 41 Avenue des Martyrs, 38027 Grenoble CEDEX 1, France. bourgeoi_at_esrf.fr}, } @ARTICLE{Breyer99, author = {W. A. Breyer and R. L. Kingston and B. F. Anderson and E. N. Baker}, title = {On the molecular-replacement problem in the presence of merohedral twinning: structure of the N-terminal half-molecule of human lactoferrin.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 1)}, pages = {129-38}, month = {January}, abstract = {The structure of a hemihedrally twinned protein crystal with two molecules in the asymmetric unit was solved by molecular replacement. The protein, a site-specific mutant of the N-terminal half-molecule of human lactoferrin, is able to undergo an internal rigid-body domain motion. Therefore, determining the structure required the independent positioning of four protein domains. The molecular-replacement solutions were obtained using a conventional real-space rotation function, and a translation function based on the linear correlation coefficient. Once the molecules were positioned, it was necessary to assign them to the appropriate twin domain. Several methods for doing this are described, one of which leads to a determination of the volume of each twin domain. In the appendix to the paper we discuss the interpretation of the self-rotation function in the presence of merohedral twinning.}, keywords = {Crystallography, X-Ray Human Lactoferrin/*chemistry/genetics Models, Molecular Mutagenesis, Site-Directed Peptide Fragments/chemistry/genetics Protein Conformation Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.}, affiliation = {Department of Biochemistry, Massey University, New Zealand.}, } @ARTICLE{Bricogne88, author = {G. Bricogne}, title = {A bayesian statistical theory of the phase problem. I. A multichannel maximum-entropy formalism for constructing generalized joint probability distributions of structure factors}, journal = {Acta Cryst A}, year = {1988}, volume = {44}, pages = {517-45}, } @ARTICLE{Bricogne90, author = {G. Bricogne}, title = {A multisolution method of phase determination by combined maximization of entropy and likelihood. I. Theory, algorithms and strategy}, journal = {Acta Cryst A}, year = {1990}, volume = {46}, pages = {284-97}, } @ARTICLE{Brunger87, author = {A. T. Brunger and J. Kuriyan and M. Karplus}, title = {Crystallographic R factor refinement by molecular dynamics}, journal = {Science}, year = {1987}, volume = {235}, number = {4787}, pages = {458-60}, month = {Jan 23}, } @ARTICLE{Brunger92, author = {A. T. Brünger}, title = {Free R value: a novel statistical quantity for assesssing the accuracy of crystal structures}, journal = {Nature}, year = {1992}, volume = {355}, number = {6359}, pages = {472-5}, month = {Jan 30}, } @ARTICLE{Brunger97, author = {A. T. Brünger}, title = {Free R value: cross-validation in crystallography}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {366-96}, } @ARTICLE{Brunger97a, author = {A. T. Brünger and L. M. Rice}, title = {Crystallographic refinement by simulated annealing: Methods and applications}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {243-69}, } @ARTICLE{Brzozowski01, author = {A. M. Brzozowski and J. Walton}, title = {Clear strategy screens for macromolecular crystallization}, journal = {J Appl Cryst}, year = {2001}, volume = {34}, pages = {97-101}, } @ARTICLE{Bunick00, author = {C. Bunick and A. C. North and G. Stubbs}, title = {Evaporative microdialysis: an effective improvement in an established method of protein crystallization.}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 11)}, pages = {1430-1}, month = {November}, abstract = {Evaporative dialysis is a simple variant of conventional microdialysis in which the reservoir solution is allowed to evaporate slowly. The slow increase in precipitant concentration allows crystals to grow without increasing nucleation. The method is useful for proteins that have a very narrow metastable zone (the range of solution conditions under which crystals grow but nuclei do not form at an appreciable rate). The method is demonstrated with the coat protein of potato virus X.}, keywords = {Capsid/*chemistry *Crystallization Microdialysis/*methods Muramidase/*chemistry Support, U.S. Gov't, Non-P.H.S.}, affiliation = {Department of Molecular Biology, Vanderbilt University, Box 1820, Station B, Nashville, Tennessee 37235, USA.}, } @ARTICLE{Burla00, author = {M. C. Burla and M. Camalli and B. Carrozzini and G. L. Cascarano and C. Giacovazzo and G. Polidori and R. Spagna}, title = {SIR2000, a program for the automatic ab initio crystal structure solution of proteins.}, journal = {Acta Cryst A}, year = {2000}, volume = {56 ( Pt 5)}, pages = {451-7}, month = {September}, abstract = {A new phasing procedure is described working both in direct and in reciprocal space. The procedure has been implemented into the program SIR2000, the heir to SIR99, and it is able routinely to solve ab initio crystal structures of proteins without any use of prior information and any user intervention. The moduli and the flow diagram of SIR2000 are also described and its efficiency tested on several protein diffraction data sets. Success has been attained for crystal structures with up to almost 2000 non-hydrogen atoms in the asymmetric unit and resolution higher than 1.2 A. The phasing process is analysed to provide a better insight into the role of the various steps of the procedure.}, keywords = {Crystallography/methods Enzymes/*chemistry Proteins/*chemistry *Software Solutions}, affiliation = {Dipartimento di Scienze della Terra, Piazza Universita, 06100 Perugia, Italy.}, } @ARTICLE{Carter79, author = {C. W. Carter Jr. and C. W. Carter}, title = {Protein crystallization using incomplete factorial experiments.}, journal = {J Biol Chem}, year = {1979}, volume = {254}, number = {23}, pages = {12219-23}, month = {Dec 10}, keywords = {Adenosine Triphosphate *Amino Acyl-tRNA Ligases Bacillus stearothermophilus/*enzymology Cations, Divalent Crystallization Methods Protein Conformation Support, U.S. Gov't, P.H.S. *Tryptophan-tRNA Ligase}, } @ARTICLE{Carter88, author = {C. W. Carter Jr. and C. W. Carter}, title = {Statistical design of experimets for protein crystal growth and the use of precrystallization assay}, journal = {Journal of Crystal Growth}, year = {1988}, volume = {90}, pages = {60-73}, } @ARTICLE{Carter94, author = {C. W. Carter Jr. and Y. Yin}, title = {Quantitative analysis in the characterization and optimization of protein crystal growth}, journal = {Acta Cryst D}, year = {1994}, volume = {50}, pages = {572-90}, } @ARTICLE{Carugo97, author = {O. Carugo and P. Argos}, title = {Protein-protein crystal-packing contacts.}, journal = {Protein Sci}, year = {1997}, volume = {6}, number = {10}, pages = {2261-3}, month = {October}, abstract = {Protein-protein contacts in monomeric protein crystal structures have been analyzed and compared to the physiological protein-protein contacts in oligomerization. A number of features differentiate the crystal-packing contacts from the natural contacts occurring in multimeric proteins. The area of the protein surface patches involved in packing contacts is generally smaller and its amino acid composition is indistinguishable from that of the protein surface accessible to the solvent. The fraction of protein surface in crystal contacts is very variable and independent of the number of packing contacts. The thermal motion at the crystal packing interface and that of the protein core, even for large packing interfaces, though the tendency is to be closer to that of the core. These results suggest that protein crystallization depends on random protein-protein interactions, which have little in common with physiological protein-protein recognition processes, and that the possibility of engineering macromolecular crystallization to improve crystal quality could be widened.}, keywords = {Crystallization Crystallography, X-Ray Macromolecular Systems Proteins/*chemistry Thermodynamics}, affiliation = {European Molecular Biology Laboratory, Heidelberg, Germany. carugo_at_embl-heidelberg.de}, } @ARTICLE{Castellano92, author = {E. E. Castellano and G. Oliva and J. Navaza}, title = {Fast rigid-body refinement for molecular-replacement techniques}, journal = {J Appl Cryst}, year = {1992}, volume = {25}, pages = {281-4}, } @ARTICLE{CCP494, author = {Collaborative-Computational-Project-Number-4}, title = {The CCP4 Suite: Programs for Protein Crystallography}, journal = {Acta Cryst D}, year = {1994}, volume = {50}, pages = {760-3}, } @ARTICLE{Chandra99, author = {N. Chandra and K. R. Acharya and P. C. Moody}, title = {Analysis and characterization of data from twinned crystals.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1750-8}, month = {October}, abstract = {It is difficult but not impossible to determine a macromolecular structure using X-ray data obtained from twinned crystals, providing it is noticed and corrected. For perfectly twinned crystals, the structure can probably only be solved by molecular replacement. It is possible to detect and characterize twinning from an analysis of the intensity statistics and crystal packing density. Tables of likely twinning operators and some examples are discussed here.}, keywords = {Algorithms Crystallization Crystallography, X-Ray/*methods Escherichia coli/enzymology Lactalbumin/chemistry Macromolecular Systems Nucleotidyltransferases/chemistry Software Support, Non-U.S. Gov't}, affiliation = {Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, England. nc42_at_le.ac.uk}, } @ARTICLE{Chayen92, author = {N. E. Chayen and P. D. S. Stewart and D. M. Blow}, title = {Microbatch crystallization under oil - a new technique allowing many small-volume crystallization trials}, journal = {Journal of Crystal Growth}, year = {1992}, volume = {122}, pages = {176-180}, } @ARTICLE{Chen00, author = {Y. W. Chen and E. J. Dodson and G. J. Kleywegt}, title = {Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures.}, journal = {Structure Fold Des}, year = {2000}, volume = {8}, number = {11}, pages = {R213-20}, month = {Nov 15}, keywords = {Animal Ciliophora/chemistry Crystallization Crystallography, X-Ray/*methods DNA-Binding Proteins/chemistry Human *Magnetic Resonance Spectroscopy Membrane Proteins/chemistry Nuclear Proteins/chemistry *Protein Conformation Protozoan Proteins/chemistry Support, Non-U.S. Gov't}, affiliation = {Centre for Protein Engineering and Cambridge University Chemical Laboratory, MRC Centre Hills Road CB2 2QH, Cambridge, United Kingdom. ywc_at_mrc-lmb.cam.ac.uk}, } @ARTICLE{Chen99, author = {Z. Chen and E. Blanc and M. S. Chapman}, title = {Improved free R factors for cross-validation of macromolecular structure - importance for real-space refinement.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 1)}, pages = {219-24}, month = {January}, abstract = {Improvements in free R cross-validation are based on changed scaling procedures and the use, in map calculation, of estimates of the validation amplitudes which are independent of the actual observed values. The deleterious effects of the omitted test data are mitigated by reduction of the test-set size, which is made possible by constraining test and working sets to share the same scaling coefficients, thereby reducing the degrees of freedom and the dependence of free R on data selection. Further improvements come with use of a modified free R factor, R freeTA. Instead of omitting the validation reflections from map calculation, their amplitudes are replaced by the average of resolution peers that is (nearly) independent of the actual cross-validation amplitudes. The improvements are relevant to model building, phase refinement by density modification and especially to real-space refinement. Although for real data at about 3 A resolution, free R factors of about 0.25 are affected little, the precision of the structure is improved by about 0.1 A. Tests with simulated data show that with good agreement between observed and calculated amplitudes (as in very high resolution studies or simulated refinement tests), free R factors can be improved by factors greater than two.}, keywords = {*Crystallography, X-Ray Data Interpretation, Statistical Macromolecular Systems Proteins/chemistry Reproducibility of Results Support, U.S. Gov't, Non-P.H.S.}, affiliation = {Department of Chemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-3015, USA.}, } @INPROCEEDINGS{Chimera96, author = {C. C. Huang and G. S. Couch and E. F. Pettersen and T. E. Ferrin}, title = {Chimera: An Extensible Molecular Modeling Application Constructed Using Standard Components.}, booktitle = {Pacific Symposium on Biocomputing}, year = {1996}, volume = { 1}, pages = {724}, owner = {miguel}, } @ARTICLE{Cowtan98, author = {K. Cowtan}, title = {Modified phased translation functions and their application to molecular-fragment location.}, journal = {Acta Cryst D}, year = {1998}, volume = {54 ( Pt 5)}, pages = {750-6}, month = {Sep 1}, abstract = {Direct methods at high resolution have depended on the resolution of atomic like features in the map. At data resolutions more typical for protein structures (2-3 A) individual atoms may not be resolved, so larger features must be identified. At one extreme the whole molecule may be located using the diffraction magnitudes alone by the molecular-replacement method. At the other extreme it is possible to locate individual residues in a well phased map. In this paper an intermediate problem is addressed: the location of multi-residue fragments on the basis of weak phase information. An agreement function based on the mean-squared difference between model and map over a masked region is shown to be more effective than a simple overlap integral, and may be efficiently calculated by Fourier methods. The techniques are compared using poorly phased electron-density maps at approximately 3 A for the proteins RNAse and O6-methylguanine-DNA-methyltransferase.}, keywords = {Animal *Computer Simulation *Crystallography, X-Ray Fourier Analysis *Models, Molecular O(6)-Methylguanine-DNA Methyltransferase/chemistry *Protein Conformation Ribonucleases/chemistry Support, Non-U.S. Gov't}, affiliation = {Department of Chemistry, University of York, Heslington, York YO1 5DD, England. cowtan_at_yorvik.york.ac.uk}, } @ARTICLE{Dauter01, author = {Z. Dauter and M. Li and A. Wlodawer}, title = {Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics.}, journal = {Acta Cryst D}, year = {2001}, volume = {57}, number = {Pt 2}, pages = {239-49}, month = {February}, abstract = {The crystal structure of pepstatin-insensitive carboxyl proteinase (PCP) from Pseudomonas sp. 101, an enzyme with no overall sequence similarity to any other proteinases of known structure, was solved using crystals soaked in sodium bromide solution and then cryocooled. A data set collected at the bromine peak absorption wavelength was sufficient for calculation of an excellent map and the entire process of phasing and tracing the maps required almost no direct human intervention. The process of structure solution using single-wavelength data was compared with three-wavelength multiwavelength anomalous diffraction (MAD); although the latter resulted in slightly better maps, the use of this much more labor-intensive approach did not significantly improve the ability to solve the structure. The successful phasing approaches are compared with several less successful attempts utilizing other crystal forms of the enzyme and the practical aspects of the use of bromine as a heavy-atom derivative are discussed. In conclusion, the use of halides with single-wavelength diffraction data fulfills the requirements of being a first-choice method of high-throughput structure solution for the emerging field of structural genomics.}, keywords = {Aspartic Endopeptidases/*chemistry Bromides Crystallography, X-Ray Genomics/*methods Indicators and Reagents Models, Molecular Protein Conformation Pseudomonas/*enzymology Sodium Compounds}, affiliation = {Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, Program in Structural Biology, National Cancer Institute and NSLS, Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973, USA. dauter_at_bnl.gov}, } @ARTICLE{Dauter97, author = {Z. Dauter}, title = {Data collection strategy}, journal = {Methods in Enzymology}, year = {1997}, volume = {276}, pages = {326-44}, } @ARTICLE{Dauter99, author = {Z. Dauter}, title = {Data-collection strategies.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1703-17}, month = {October}, abstract = {The optimal strategy for collecting X-ray diffraction data from macromolecular crystals is discussed. Two kinds of factors influencing the completeness of data are considered. The first are geometric, arising from the symmetry of the reciprocal lattice and from the experimental setup; they affect quantitatively the completeness of the measured set of reflections. The second concern the quality, or information content, of the recorded intensities of these measured reflections.}, keywords = {*Automatic Data Processing *Crystallography, X-Ray Macromolecular Systems Muramidase/chemistry}, affiliation = {National Cancer Institute, Frederick and Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973, USA. dauter_at_bnl.gov}, } @BOOK{Delano02, title = {The PyMOL molecular graphics system}, publisher = {Delano Scientific}, year = {2002}, author = {W. L. Delano}, address = {San Carlos, CA}, owner = {miguel}, } @ARTICLE{Delarue00, author = {M. Delarue and H. Orland}, title = {General formalism for phase combination and phase refinement: a statistical thermodynamics approach in reciprocal space.}, journal = {Acta Crystallogr A}, year = {2000}, volume = {56 ( Pt 6)}, pages = {562-74}, month = {November}, abstract = {The mean-field optimization methodology has been used to recast in a single formalism the problem of phase optimization using an arbitrary energy function in the presence of an experimentally determined phase probability distribution function. It results naturally in the generalization of the notions of figure of merit and centroid phase where the weight of the energy refinement is controlled by an effective temperature in a self-consistent manner. In the limit of high temperature, the formalism reduces of course to the Blow \& Crick [Acta Cryst. (1959), 12, 794-802] classical treatment. If a model is available, Sim's [Acta Cryst. (1960), 13, 511-512] weighting scheme for a combined map appears as the first step of a refinement to be conducted until self-consistency is achieved. Assuming that MIR phases exist and that they agree reasonably well with the phases of the model, a first-order expansion gives an estimate of the changes of weights and phases to be performed for the Fourier synthesis. This provides for a new way of doing phase combination that might prove useful in challenging cases of model refinement, e.g. in large macromolecular complexes. Thermodynamic considerations have been used to discuss the best determination of weights in phase refinement; they also suggest that a variational expression of maximum likelihood is best suited as a target for refinement because it is the free energy of the system. The formalism readily allows use of solvent flattening, density averaging and the atomicity criterion to refine phases, and automatically assigns a figure of merit to each reflection. Numerical tests of the method are presented in an attempt to resolve the phase-ambiguity problem of protein crystallography in the centrosymmetric P?1? space group using an energy derived from the Sayre equation.}, keywords = {*Biopolymers Fourier Analysis Likelihood Functions Macromolecular Systems Models, Theoretical Molecular Conformation *Thermodynamics X-Ray Diffraction/methods}, affiliation = {Unite de Biochimie Structurale, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France. delarue_at_pasteur.fr}, } @ARTICLE{Delphi90, author = {K. A. Sharp and B. Honig}, title = {Electrostatic interactions in macromolecules: theory and applications.}, journal = {Annu Rev Biophys Biophys Chem}, year = {1990}, volume = {19}, pages = {301-32}, keywords = {Biophysics *Electrochemistry *Macromolecular Systems Models, Theoretical Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.}, affiliation = {Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.}, } @ARTICLE{Diederichs97, author = {K. Diederichs and P. A. Karplus}, title = {Improved R-factors for diffraction data analysis in macromolecular crystallography.}, journal = {Nat Struct Biol}, year = {1997}, volume = {4}, number = {4}, pages = {269-75}, month = {April}, abstract = {The quantity Rsym (also called Rmerge) is almost universally used for describing X-ray diffraction data quality. Here, we prove that Rsym is seriously flawed, because it has an implicit dependence on the redundance of the data. A corrected R-factor, Rmeas, is introduced as the equivalent robust indicator of data consistency. In addition, we introduce Rmrgd an R-factor that reflects the gain in accuracy upon averaging of equivalent reflections, as a useful indicator of the quality of reduced data. These new data quality indicators better reveal the benefits of highly redundant data and should stimulate improvements in data quality through increased merging of data from multiple crystals.}, keywords = {Crystallography, X-Ray/*methods Fourier Analysis *Models, Statistical Reproducibility of Results Software Statistics Urease/chemistry}, affiliation = {Universitat Konstanz, Fakultat fur Biologie, Germany.}, } @ARTICLE{Dodson98, author = {E. Dodson}, title = {The role of validation in macromolecular crystallography.}, journal = {Acta Cryst D}, year = {1998}, volume = {54}, number = {1 ( Pt 6)}, pages = {1109-18}, month = {Nov 1}, abstract = {The importance of validation techniques in X-ray structure determination and their relation to refinement procedures are discussed, with particular reference to atomic resolution structures. The requirements of deposition and publication, and the role of validation tools in this are analysed. The need for a rigorously defined file format is emphasized.}, keywords = {*Crystallography, X-Ray *Protein Conformation Reproducibility of Results Support, Non-U.S. Gov't User-Computer Interface}, affiliation = {Department of Chemistry, University of York, Heslington, York YO1 5DD, England.ccp4_at_yorvic.york.ac.uk}, } @ARTICLE{Dorset00, author = {D. L. Dorset}, title = {On the direct determination of three-dimensional crystallographic phases at low resolution: crambin at 6 A.}, journal = {Proc Natl Acad Sci U S A}, year = {2000}, volume = {97}, number = {8}, pages = {3982-6}, month = {Apr 11}, abstract = {Using a pseudo-atom approach, the three-dimensional crystallographic phases for the protein crambin (a = 40.76, b = 18.49, c = 22.33 A, beta = 90.61 degrees, space group P2(1)) were determined to 6 A by direct methods. First, the centrosymmetric h0l set was assigned phases by symbolic addition, and the initial solution was then refined by Fourier methods. Phase values of strong reflections were then permuted, and the decision to change the phase value for two of these was made by consulting a cross-correlation of the experimental density histogram to the theoretical or known histogram for the protein. The two-dimensional basis was then extended by the Sayre equation into three dimensions by assigning a phase to a third allowed hkl origin-defining reflection and an algebraic value to another axial reflection. The correct solution was again identified by the histogram correlation, yielding a solution in which the mean phase error for all 98 reflections was 61.5 degrees or 23.1 degrees for the 21 most intense reflections. A parallel study with another protein indicates this method may have general utility.}, keywords = {Crystallography, X-Ray Plant Proteins/*chemistry Protein Conformation Support, U.S. Gov't, P.H.S.}, affiliation = {Electron Diffraction Department, Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, NY 14203-1196, USA. dorset_at_hwi.buffalo.edu}, } @ARTICLE{Ducruix90, author = {A. F. Ducruix and M. M. Ries-Kautt}, title = {Solubility diagram analysis and the relative effectiveness of different ions on protein crystal growth}, journal = {Methods}, year = {1990}, volume = {1}, number = {1}, pages = {25-30}, month = {August}, } @ARTICLE{Emsley04, author = {Paul Emsley and Kevin Cowtan}, title = {Coot: Model-Building Tools for Molecular Graphics}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {2004}, pages = {(in press)}, owner = {miguel}, } @ARTICLE{EU3D98, author = {no_authors_listed}, title = {Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.}, journal = {J Mol Biol}, year = {1998}, volume = {276}, number = {2}, pages = {417-36}, month = {Feb 20}, abstract = {Eight protein crystal structures, which have been refined against X-ray diffraction data extending to atomic resolution, 1.2 A or better, were inspected using four different validation tools, PROCHECK, PROVE, SQUID and WHATCHECK. Two general questions were addressed. (1) Do the structures imply changes in "expected" stereochemical properties and are the target values used for restraints in the validation programs and the refinement protocol appropriate? (2) Can errors in models be detected and how reliable are the coordinates after refinement? Preliminary analysis by members of the network led to modifications both to the validation programs and to the refinement protocols. The results of the final analyses are reported here. Apparent discrepancies in cell dimensions were identified. Most stereochemical properties are shown to be more tightly clustered than for lower resolution analyses. In contrast the omega angle has a wider distribution. The validation software is generally available and can be accessed at servers listed at the end of the paper.}, keywords = {Crystallography, X-Ray Hydrogen Bonding Isoenzymes/chemistry *Models, Molecular Proline/chemistry Protein Conformation Proteins/*chemistry Reproducibility of Results Ribonucleases/chemistry Rubredoxins/chemistry *Software Solvents Support, Non-U.S. Gov't}, } @ARTICLE{Evans00, author = {G. Evans and R. R. Pettifer}, title = {CHOOCH: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra}, journal = {J Appl Cryst}, year = {2000}, volume = {34}, pages = {82-6}, } @ARTICLE{Evans99, author = {P. R. Evans}, title = {Some notes on choices in data collection.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1771-2}, month = {October}, abstract = {Collecting optimum X-ray diffraction data involves a number of choices and compromises, including choice of crystal, source, rotation range, exposure time and programs for integration and scaling. This paper presents a series of questions which should be considered in planning a data-collection experiment.}, keywords = {X-Ray Diffraction/instrumentation/*methods}, affiliation = {MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England. pre_at_mrc-lmb.cam.ac.uk}, } @ARTICLE{Fernandez00, author = {E. J. Fernández and A. Joachimiak and E. Lolis}, title = {A cryocooling technique for protein crystals grown by dialysis from volatile solvents}, journal = {J Appl Cryst}, year = {2000}, volume = {33}, pages = {168-71}, } @ARTICLE{French78, author = {S. French and K. Wilson}, title = {On the treatment of negative intesity observations}, journal = {Acta Cryst A}, year = {1978}, volume = {34}, pages = {517-25}, } @ARTICLE{Garman97, author = {E. F. Garman and T. R. Schneider}, title = {Macromolecular cryocrystallography}, journal = {J Appl Cryst}, year = {1997}, volume = {30}, pages = {211-37}, } @ARTICLE{Garman99, author = {E. Garman}, title = {Cool data: quantity AND quality.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1641-53}, month = {October}, abstract = {The use of cryo-techniques in macromolecular crystallography has increased enormously over the last eight years and has become a vital part of modern X-ray data-collection methods. This paper presents some reasons for the rise in popularity of cryo-techniques and a brief outline of the basic methods, followed by a detailed discussion of factors to be considered when trying to optimize both the quantity and quality of the data collected. As more experimenters at synchrotrons observe significant radiation damage to crystals held near 100 K, the available options for further prolonging crystal lifetime and extending the techniques become worth investigating. Some possibilities and parameters to be considered are presented, although these must remain speculative until more experimental data are available.}, keywords = {Crystallization Crystallography, X-Ray/*methods Cyclin-Dependent Kinases/chemistry Cytochromes/chemistry Freezing Glycerol/chemistry Neuraminidase/chemistry Nitrite Reductases/chemistry Osmolar Concentration Protein-Serine-Threonine Kinases/chemistry Ribonuclease, Pancreatic/chemistry Salmonella typhimurium/enzymology Software Support, Non-U.S. Gov't Water/chemistry}, affiliation = {Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England. elspeth_at_biop.ox.ac.uk}, } @ARTICLE{George94, author = {A. George and W. W. Wilson}, title = {Predicting protein crystallization for dilute solution property}, journal = {Acta Cryst D}, year = {1994}, volume = {50}, pages = {361-5}, } @ARTICLE{Gonzalez01, author = {A. Gonzalez and G. Larsson and R. Persson and E. Cedergren-Zeppezauer}, title = {Atomic resolution structure of Escherichia coli dUTPase determined ab initio.}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {2001}, volume = {57}, number = {Pt 6}, pages = {767-74}, month = {June}, abstract = {Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 A resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 A from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14\% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution.}, affiliation = {European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany. ana_at_slac.stanford.edu}, } @ARTICLE{Grasp91, author = {A. Nicholls and K. A. Sharp and B. Honig}, title = {Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.}, journal = {Proteins}, year = {1991}, volume = {11}, number = {4}, pages = {281-96}, abstract = {We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.}, keywords = {Algorithms Hydrocarbons/*chemistry *Protein Binding *Protein Conformation Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. Surface Tension Thermodynamics}, affiliation = {Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032.}, } @ARTICLE{Gu01, author = {Y. X. Gu and Y. D. Liu and Q. Hao and S. E. Ealick and H. F. Fan}, title = {Direct-method-aided phasing of MAD data.}, journal = {Acta Cryst D}, year = {2001}, volume = {57}, number = {Pt 2}, pages = {250-3}, month = {February}, abstract = {The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 A resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607--15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5 degrees and improved map connectivity.}, keywords = {Adenosine Kinase/*chemistry Comparative Study Crystallography, X-Ray/*methods Data Interpretation, Statistical Human *Models, Molecular Protein Conformation Scattering, Radiation Support, Non-U.S. Gov't}, affiliation = {Institute of Physics, Chinese Academy of Sciences, Beijing 100080, People's Republic of China.}, } @ARTICLE{Harding01, author = {M. M. Harding}, title = {Geometry of metal-ligand interactions in proteins.}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {2001}, volume = {57}, number = {Pt 3}, pages = {401-11}, month = {March}, abstract = {The geometry of metal-ligand interactions in proteins is examined and compared with information for small-molecule complexes from the Cambridge Structural Database (CSD). The paper deals with the metals Ca, Mg, Mn, Fe, Cu, Zn and with metal-donor atom distances, coordination numbers and extent of distortion from ideal geometry (octahedral, tetrahedral etc.). It assesses the agreement between geometry found in all metalloprotein structures in the Protein Data Bank (PDB) determined at resolution $<$ or = 1.6 A with that predicted from the CSD for ligands which are analogues of amino-acid side chains in proteins [Harding (1999), Acta Cryst. D55, 1432-1443; Harding (2000), Acta Cryst. D56, 857-867]. The agreement is reasonably good for these structures but poorer for many determined at lower resolution (examined to 2.8 A resolution). For metal-donor distances, the predictions from the CSD, with minor adjustments, provide good targets either for validation or for restraints in refinement of structures where only poorer resolution data is available. These target distances are tabulated and the use of restraints is recommended. Validation of angles or the use in refinement of restraints on angles at the metal atom is more difficult because of the inherent flexibility of these angles. A much simplified set of parameters for angle restraints with quite large standard deviations is provided. (Despite the flexibility of the angles, acceptable and preferred coordination numbers and shapes are well established and a summary table is provided.) An unusual and perhaps biochemically important feature of Zn coordination with carboxylate seen in the CSD examples is also clearly present in metalloprotein structures. With metals like Ca, carboxylate coordination is monodentate or bidentate (two M-O bonds of nearly equal length). In Zn carboxylates a continuous range between monodentate and bidentate coordination is found, with one Zn-O bond of normal length and another of any length between this and a van der Waals contact.}, keywords = {Amino Acids/chemistry Carboxylic Acids/chemistry Databases, Factual Ligands Metals/*chemistry Protein Conformation Proteins/*chemistry Reproducibility of Results Zinc/chemistry}, affiliation = {Institute of Cell and Molecular Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3JR, Scotland. marjorie.harding_at_ed.ac.uk}, } @ARTICLE{Harp98, author = {J. M. Harp and D. E. Timm and G. J. Bunick}, title = {Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography.}, journal = {Acta Cryst D}, year = {1998}, volume = {54 ( Pt 4)}, pages = {622-8}, month = {Jul 1}, abstract = {Although cryogenic data collection has become the method of choice for macromolecular crystallography, the flash-cooling step can dramatically increase the mosaicity of some crystals. Macromolecular crystal annealing significantly reduces the mosaicity of flash-cooled crystals without affecting molecular structure. The process, which cycles a flash-cooled crystal to ambient temperature and back to cryogenic temperature, is simple, quick and requires no special equipment. The annealing process has been applied to crystals of several different macromolecules grown from different precipitants and using a variety of cryoprotectants. The protocol for macromolecular crystal annealing also has been applied to restore diffraction from flash-cooled crystals that were mishandled during transfer to or from cryogenic storage. These results will be discussed in relation to crystal mosaicity and effects of radiation damage in flash-cooled crystals.}, keywords = {Crystallization Crystallography, X-Ray/*methods Freezing Histones/chemistry Human Muramidase/chemistry Nucleosomes/chemistry Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.}, affiliation = {University of Tennessee/Oak Ridge Graduate School of Biomedical Sciences, Oak Ridge, TN 37831-8080, USA.}, } @ARTICLE{Hennessy00, author = {D. Hennessy and B. Buchanan and D. Subramanian and P. A. Wilkosz and J. M. Rosenberg}, title = {Statistical methods for the objective design of screening procedures for macromolecular crystallization.}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 7)}, pages = {817-27}, month = {July}, abstract = {The crystallization of a new macromolecule is still very much a trial-and-error process. As is well known, it requires the search of a large parameter space of experimental settings to find the relatively few idiosyncratic conditions that lead to diffraction-quality crystals. Crystallographers have developed a variety of screens to help identify initial crystallization conditions, including those based on systematic grids, incomplete factorial and sparse-matrix approaches. These are somewhat subjectively formulated based on accumulated data from past crystallization experiments. Ideally, one would prefer as objective a procedure as possible; however, that requires objective methods that incorporate a broad source of crystallization data. The Biological Macromolecular Crystallization Database (BMCD), a repository of all published crystallization conditions, is an obvious source of this data. This database has been augmented with a hierarchical classification of the macromolecules contained in the BMCD as well as extensive data on the additives used with them. A statistical analysis of the augmented BMCD shows the existence of significant correlations between families of macromolecules and the experimental conditions under which they crystallize. This in turn leads to a Bayesian technique for determining the probability of success of a set of experimental conditions based on the data in the BMCD as well as facts about a macromolecule known prior to crystallization. This has been incorporated into software that enables users to rank experimental conditions for new macromolecules generated by a dense partial factorial design. Finally, an additional advantage of the software described here is that it also facilitates the accumulation of the data required for improving the accuracy of estimation of the probabilities of success - knowledge of the conditions which lead to failure of crystallization.}, keywords = {*Crystallization Databases, Factual *Macromolecular Systems Statistics Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.}, affiliation = {Intelligent Systems Laboratory, University of Pittsburgh, Pittsburgh, PA 15260, USA.}, } @ARTICLE{Holm99, author = {L Holm and C Sander}, title = {Protein folds and families: sequence and structure alignments.}, journal = {Nucleic Acids Res}, year = {1999}, volume = {27}, number = {1}, pages = {244-7}, month = {Jan}, pii = {gkc097}, abstract = {Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36\% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/}, owner = {miguel}, keywords = {Databases, Factual, Evolution, Molecular, Information Storage and Retrieval, Internet, Protein Conformation, Protein Folding, Proteins, Reproducibility of Results, Sequence Alignment, Sequence Homology, Amino Acid, Variation (Genetics), 9847191}, } @ARTICLE{Housset00, author = {D. Housset and F. Benabicha and V. Pichon-Pesme and C. Jelsch and A. Maierhofer and S. David and J. C. Fontecilla-Camps and C. Lecomte}, title = {Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 A resolution as a first test case.}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 2)}, pages = {151-60}, month = {February}, abstract = {The number of protein structures refined at a resolution higher than 1.0 A is continuously increasing. Subatomic structures may deserve a more sophisticated model than the spherical atomic electron density. In very high resolution structural studies (d $<$ 0.5 A) of small peptides, a multipolar atom model is used to describe the valence electron density. This allows a much more accurate determination of the anisotropic thermal displacement parameters and the estimate of atomic charges. This information is of paramount importance in the understanding of biological processes involving enzymes and metalloproteins. The structure of the scorpion Androctonus australis Hector toxin II has been refined at 0.96 A resolution using synchrotron diffraction data collected at room temperature. Refinement with a multipolar electron-density model in which the multipole populations are transferred from previous peptide studies led to the observation of valence electrons on covalent bonds of the most ordered residues. The refined net charges of the peptide-bond atoms were of the correct sign but were underestimated. Such protein-structure refinements against higher resolution data collected at cryogenic temperature will enable the calculation of experimental atomic charges and properties such as electrostatic potentials.}, keywords = {Crystallography, X-Ray Models, Molecular Neurotoxins/*chemistry Protein Conformation Scorpion Venoms/*chemistry Software Temperature Thermodynamics}, affiliation = {Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale 'Jean-Pierre Ebel', CEA-CNRS, 41 Rue Jules Horowitz, F-38027 Grenoble CEDEX 1, France.}, } @ARTICLE{Jelsch00, author = {C. Jelsch and M. M. Teeter and V. Lamzin and V. Pichon-Pesme and R. H. Blessing and C. Lecomte}, title = {Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.}, journal = {Proc Natl Acad Sci U S A}, year = {2000}, volume = {97}, number = {7}, pages = {3171-6}, month = {Mar 28}, abstract = {The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25\% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.}, keywords = {Crystallography, X-Ray Electrons Plant Proteins/*chemistry Protein Conformation Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.}, affiliation = {Laboratoire de Cristallographie et Modelisation des Materiaux Mineraux et Biologiques, Universite Henri Poincare-Nancy 1-Centre National de la Recherche Scientifique ESA 7036, BP 239, 54506 Vandoeuvre-les-Nancy, France.}, } @ARTICLE{Kabsch83, author = {W. Kabsch and C. Sander}, title = {Dictionary of protein secondary structure -- pattern-recognition of hydrogen-bonded and geometrical features.}, journal = {Biopolymers}, year = {1983}, volume = {22}, pages = {2577-2637}, owner = {miguel}, } @ARTICLE{Kiefersauer00, author = {R. Kieffersauer and M. Than and H. Dobbek and L. Gremer and M. Melero and S. Strobl and J. M. Dias and T. Soulimane and R. Huber}, title = {A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidty changes}, journal = {J Appl Cryst}, year = {2000}, volume = {33}, pages = {1223-30}, } @ARTICLE{Kleywegt00, author = {G. J. Kleywegt}, title = {Validation of protein crystal structures.}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 3)}, pages = {249-65}, month = {March}, abstract = {Since the process of building and refining a model of a biomacromolecule based on crystallographic data is subjective, quality-control techniques are required to assess the validity of such models. During the 1990s, much experience was gained; the methods used and some of the lessons learned are reviewed here. In addition, an extensive compendium of quality criteria and quality-control methods that are or have been used to validate models of biomacromolecules has been compiled. The emphasis in this compendium is on the validation of protein crystal structures.}, keywords = {Biochemistry/education *Crystallography, X-Ray Evaluation Studies Human Magnetic Resonance Spectroscopy Models, Molecular Observer Variation *Protein Conformation Support, Non-U.S. Gov't}, affiliation = {Department of Cell Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden. gerard_at_xray.bmc.uu.se}, } @ARTICLE{Kleywegt95, author = {G. J. Kleywegt and T. A. Jones}, title = {Where freedom is given, liberties are taken.}, journal = {Structure}, year = {1995}, volume = {3}, number = {6}, pages = {535-40}, month = {Jun 15}, keywords = {*Crystallography, X-Ray *Models, Molecular R Factors/*chemistry Software}, affiliation = {Department of Molecular Biology, Uppsala University, Sweden.}, } @ARTICLE{Kleywegt96, author = {G. J. Kleywegt and A. T. Brunger}, title = {Checking your imagination: applications of the free R value.}, journal = {Structure}, year = {1996}, volume = {4}, number = {8}, pages = {897-904}, month = {Aug 15}, keywords = {Comparative Study *Crystallography, X-Ray *Data Interpretation, Statistical *Models, Chemical Molecular Structure Protein Conformation Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S.}, affiliation = {Department of Molecular Biology, Biomedical Centre, Uppsala University, Box 590, S-751 24 Uppsala, Sweden.}, } @ARTICLE{Kleywegt97, author = {G. Kleywegt and T. A. Jones}, title = {Model building and refinement practice}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {208-30}, } @ARTICLE{Kraulis91, author = {P. J. Kraulis}, title = {MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures}, journal = {Journal of Applied Crystallography}, year = {1991}, volume = {24}, pages = {946-50}, } @INPROCEEDINGS{Krissinel03, author = {E. Krissinel and K. Henrick}, title = {Protein structure comparison in 3D based on secondary structure matching (SSM) followed by Ca alignment, scored by a new structural similarity function.}, booktitle = {Proceedings of the 5th International Conference on Molecular Structural Biology}, year = {2003}, editor = {Andreas J. Kungl and Penelope J. Kungl}, pages = {88}, owner = {miguel}, } @ARTICLE{Kwong99, author = {P. D. Kwong and Y. Liu}, title = {Use of cryoprotectant in combination with immiscible oils for flash cooling macromolecular crystals}, journal = {J Appl Cryst}, year = {1999}, volume = {32}, pages = {102-5}, } @ARTICLE{Lamzin97, author = {V. S. Lamzin and K. S. Wilson}, title = {Automated refinement for protein crystallography}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {269-305}, } @ARTICLE{Langs01, author = {D. A. Langs and R. H. Blessing and D. Guo}, title = {Map self-validation: a useful discriminator of phase correctness at low resolution.}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {2001}, volume = {57}, number = {Pt 4}, pages = {574-8}, month = {April}, abstract = {A new map-validation procedure is based on the correlation-coefficient agreement between the observed structure-factor magnitudes and their extrapolated values from suitably modified electron-density maps from which they have been each in turn systematically excluded. The correlation coefficient tends to a maximum as the phase errors in a map are reduced. This principle was used to resolve the single-wavelength anomalous scattering (SAS) and single-derivative isomorphous replacement (SIR) phase ambiguity for a number of error-free trial structures. Applications employing real data sets tend to be more difficult owing to data incompleteness and errors affecting the construction of the Argand diagram.}, affiliation = {Hauptman-Woodward Medical Research Institute Inc., 73 High Street, Buffalo, NY 14203, USA. langs_at_algol.hwi.buffalo.edu}, } @ARTICLE{Lawrence93, author = {M. C. Lawrence and P. M. Colman}, title = {Shape complementarity at protein/protein interfaces.}, journal = {J Mol Biol}, year = {1993}, volume = {234}, number = {4}, pages = {946-50}, month = {Dec 20}, abstract = {A new statistic Sc, which has a number of advantages over other measures of packing, is used to examine the shape complementarity of protein/protein interfaces selected from the Brookhaven Protein Data Bank. It is shown using Sc that antibody/antigen interfaces as a whole exhibit poorer shape complementarity than is observed in other systems involving protein/protein interactions. This result can be understood in terms of the fundamentally different evolutionary history of particular antibody/antigen associations compared to other systems considered, and in terms of the differing chemical natures of the interfaces.}, keywords = {*Antigen-Antibody Reactions Hemoglobins/chemistry Immunoglobulins, Fab/chemistry Macromolecular Systems Models, Molecular Neuraminidase/chemistry *Protein Binding *Protein Conformation Proteins/*chemistry}, affiliation = {Biomolecular Research Institute, Parkville, Victoria, Australia.}, } @ARTICLE{Leslie92, author = {A. G. W. Leslie}, title = {Recent changes to the MOSFLM package for processing film and image plate data}, journal = {Joint CCP4 and ESF-EACBM Newsletters on Protein Crystallography}, year = {1992}, volume = {26}, } @ARTICLE{Leslie99, author = {A. G. Leslie}, title = {Integration of macromolecular diffraction data.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1696-702}, month = {October}, abstract = {Diffraction intensities can be evaluated by two distinct procedures: summation integration and profile fitting. Equations are derived for evaluating the intensities and their standard errors for both cases, based on Poisson statistics. These equations highlight the importance of the contribution of the X-ray background to the standard error and give an estimate of the improvement which can be achieved by profile fitting. Profile fitting offers additional advantages in allowing estimation of saturated reflections and in dealing with incompletely resolved diffraction spots.}, keywords = {Crystallography, X-Ray/*methods Macromolecular Systems Poisson Distribution Software}, affiliation = {MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England. andrew_at_mrc-lmb.cam.ac.uk}, } @ARTICLE{Li01, author = {G. Li and Y. Xiang and D. D. Wang}, title = {A simple and efficient innovation of the vapor-diffusion method for controlling nucleation and growth of large protein crystals}, journal = {J Appl Cryst}, year = {2001}, volume = {34}, pages = {388-91}, } @ARTICLE{Lin00, author = {D. Lin and N. O. Manning and J. Jiang and E. E. Abola and D. Stampf and J. Prilusky and J. L. Sussman}, title = {AutoDep: a web-based system for deposition and validation of macromolecular structural -information.}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 7)}, pages = {828-41}, month = {July}, abstract = {This paper describes the design and full implementation of a new concept in data deposition and validation: AutoDep (copyright Brookhaven Science Associates LLC). AutoDep changes the traditional procedure for data acceptance and validation of the primary databases into an interactive depositor-driven operation which almost eliminates the delay between the acceptance of the data and its public release. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators for the complete and accurate description of the structural experiment and its results. AutoDep, developed by the Protein Data Bank at Brookhaven National Laboratory (BNL) as a flexible and portable system, has already been adopted by other primary databases and implemented on different platforms/operating systems. AutoDep was introduced at BNL in 1996 [see Manning (1996), Protein Data Bank Quart. Newslett. 77, 2 (ftp://ftp.rcsb. org/pub/pdb/doc/newsletters/bnl/newsletter96jul/newslttr+ ++.txt); Manning (1996), Protein Data Bank Quart. Newslett. 78, 2 (ftp://ftp. rcsb.org/pub/pdb/doc/newsletters/bnl/newsletter96oct/+ ++newslttr.txt)].}, keywords = {Computer Security *Database Management Systems *Internet *Macromolecular Systems User-Computer Interface Vocabulary}, affiliation = {Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.}, } @ARTICLE{Lunin98, author = {V. Y. Lunin and N. L. Lunina and T. E. Petrova and A. G. Urzhumtsev and A. D. Podjarny}, title = {On the ab initio solution of the phase problem or macromolecules at very low resolution. II. Generalized likelihood based approach to cluster discrimination.}, journal = {Acta Cryst D}, year = {1998}, volume = {54 ( Pt 5)}, pages = {726-34}, month = {Sep 1}, abstract = {The multisolution strategies for direct phasing at very low resolution, such as the few atoms model technique, result in a number of alternative phase sets, each of them arising from a cluster of closely related models. Use of a Monte-Carlo type computer procedure is suggested to choose between the possible phase sets. It consists of generating a large number of pseudo-atom models inside the mask defined by a trial phase set and the use of histograms of magnitude correlation to evaluate the masks. It is shown that the procedure may be considered as a generalization of the statistical maximum-likelihood principle and may be used as a powerful supplementary tool in the likelihood-based approaches to the phase problem solution.}, keywords = {*Cluster Analysis *Computer Simulation *Crystallography, X-Ray *Likelihood Functions *Models, Molecular Monte Carlo Method Support, Non-U.S. Gov't}, affiliation = {Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142292, Russia.}, } @ARTICLE{Luzzati52, author = {V. Luzzati}, title = {Traitement statistique des erreurs dans la determination des structures cristallines}, journal = {Acta Cryst}, year = {1952}, volume = {5}, pages = {802-10}, } @ARTICLE{McRee92, author = {D. E. McRee}, title = {A visual protein crystallographic software system for X11/XView}, journal = {J Molecular Graphics}, year = {1992}, volume = {10}, pages = {44-6}, } @ARTICLE{Merritt97, author = {E. A. Merritt and D. J. Bacon}, title = {Raster3D: Photorealistic Molecular Graphics}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {505-24}, } @ARTICLE{Miller01, author = {S. T. Miller and J. M. Hogle and D. J. Filman}, title = {Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution.}, journal = {J Mol Biol}, year = {2001}, volume = {307}, number = {2}, pages = {499-512}, month = {Mar 23}, abstract = {A genetic algorithm-based computational method for the ab initio phasing of diffraction data from crystals of symmetric macromolecular structures, such as icosahedral viruses, has been implemented and applied to authentic data from the P1/Mahoney strain of poliovirus. Using only single-wavelength native diffraction data, the method is shown to be able to generate correct phases, and thus electron density, to 3.0 A resolution. Beginning with no advance knowledge of the shape of the virus and only approximate knowledge of its size, the method uses a genetic algorithm to determine coarse, low-resolution (here, 20.5 A) models of the virus that obey the known non-crystallographic symmetry (NCS) constraints. The best scoring of these models are subjected to refinement and NCS-averaging, with subsequent phase extension to high resolution (3.0 A). Initial difficulties in phase extension were overcome by measuring and including all low-resolution terms in the transform. With the low-resolution data included, the method was successful in generating essentially correct phases and electron density to 6.0 A in every one of ten trials from different models identified by the genetic algorithm. Retrospective analysis revealed that these correct high-resolution solutions converged from a range of significantly different low-resolution phase sets (average differences of 59.7 degrees below 24 A). This method represents an efficient way to determine phases for icosahedral viruses, and has the advantage of producing phases free from model bias. It is expected that the method can be extended to other protein systems with high NCS. Copyright 2001 Academic Press.}, keywords = {*Algorithms Capsid/chemistry/*ultrastructure Crystallography, X-Ray/*methods Models, Molecular Models, Structural Models, Theoretical Polioviruses/*chemistry/ultrastructure Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.}, affiliation = {Committee for Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA.}, } @ARTICLE{Minor00, author = {W. Minor and D. Tomchick and Z. Otwinowski}, title = {Strategies for macromolecular synchrotron crystallography.}, journal = {Structure Fold Des}, year = {2000}, volume = {8}, number = {5}, pages = {R105-10}, month = {May 15}, keywords = {Crystallography, X-Ray/instrumentation/*methods Internet Proteins/*chemistry Research Design Signal Processing, Computer-Assisted Support, U.S. Gov't, P.H.S. *Synchrotrons}, affiliation = {Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA. wladek_at_iwonka.med.virginia.edu.}, } @ARTICLE{Murshudov97, author = {G. N. Murshudov and A. A. Vagin and E. J. Dodson}, title = {Refinement of macromolecular structures by the maximum-likelihood method}, journal = {Acta Cryst D}, year = {1997}, volume = {53}, pages = {240-55}, } @ARTICLE{Murshudov99, author = {G. N. Murshudov and A. A. Vagin and A. Lebedev and K. S. Wilson and E. J. Dodson}, title = {Efficient anisotropic refinement of macromolecular structures using FFT.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 1)}, pages = {247-55}, month = {January}, abstract = {This paper gives the equations for the use of fast Fourier transformations in individual atomic anisotropic refinement. Restraints on bonded atoms, on the sphericity of each atom and between non-crystallographic symmetry related atoms are described. These have been implemented in the program REFMAC and its performance with several examples is analysed. All the tests show that anisotropic refinement not only reduces the R value and Rfree but also improves the fit to geometric targets, indicating that this parameterization is valuable for improving models derived from experimental data. The computer time taken is comparable to that for isotropic refinements.}, keywords = {Catalase/chemistry *Crystallography, X-Ray *Fluorescence Polarization *Fourier Analysis Macromolecular Systems Models, Molecular Protein Conformation Ribonucleases/chemistry Software Support, Non-U.S. Gov't}, affiliation = {Chemistry Department, University of York, Heslington, York YO1 5DD, England and CLRC, Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England.garib_at_yorvic.york.ac.uk}, } @ARTICLE{Navaza94, author = {J. Navaza}, title = {AMoRe: an Automated package for Molecular Replacement}, journal = {Acta Cryst D}, year = {1994}, volume = {50}, pages = {157-63}, } @ARTICLE{Pannu96, author = {N. S. Pannu and R. J. Read}, title = {Improved structure refinement through maximum likelihood}, journal = {Acta Cryst A}, year = {1997}, volume = {52}, pages = {659-68}, } @ARTICLE{Pannu98, author = {N. S. Pannu and G. N. Murshudov and E. J. Dodson and R. J. Read}, title = {Incorporation of prior phase information strengthens maximum-likelihood structure refinement.}, journal = {Acta Cryst D}, year = {1998}, volume = {54}, number = {2 ( Pt 6)}, pages = {1285-94}, month = {Nov 1}, abstract = {The application of a maximum-likelihood analysis to the problem of structure refinement has led to striking improvements over the traditional least-squares methods. Since the method of maximum likelihood allows for a rational incorporation of other sources of information, we have derived a likelihood function that incorporates experimentally determined phase information. In a number of different test cases, this target function performs better than either a least-squares target or a maximum-likelihood function lacking prior phases. Furthermore, this target gives significantly better results compared with other functions incorporating phase information. When combined with a procedure to mask 'unexplained' density, the phased likelihood target also makes it possible to refine very incomplete models.}, keywords = {Animal Crystallography, X-Ray Cytochrome c/chemistry *Likelihood Functions Models, Molecular *Molecular Structure Protein Conformation Receptors, Estrogen/chemistry Support, Non-U.S. Gov't}, affiliation = {Department of Mathematical Sciences, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.}, } @ARTICLE{Parkin00, author = {S. Parkin}, title = {Expansion of scalar validation criteria to three dimensions: the R tensor. Erratum.}, journal = {Acta Crystallogr A}, year = {2000}, volume = {56}, number = {Pt 3}, pages = {317}, month = {May}, abstract = {In the paper by Parkin [Acta Cryst. (2000), A56, 157-162], an incorrect correspondence e-mail address is given. The correct address is given above.}, affiliation = {Biochemistry Department, Box 3711, Duke University Medical Center, Durham, NC, USA. spark2_at_pop.uky.edu}, } @ARTICLE{Parkin00a, author = {S. Parkin}, title = {Expansion of scalar validation criteria to three dimensions: the R tensor}, journal = {Acta Crystallogr A}, year = {2000}, volume = {56 (Pt 2)}, pages = {157-62}, month = {March}, abstract = {Assessment of quality in crystal structure determination entails analysis of global statistics. In data reduction, quality is assessed using R(merge) and mean I/sigma(I). Progress in structure solution and refinement is checked by the goodness of fit, variants of the R index, R(cryst), and its cross-validation counterpart, R(free). These statistics are useful and provide a convenient means of comparison but their scalar nature renders them unable to capture the essence of three-dimensional entities such as diffraction patterns and molecular models. A simple general method to quantify spatial variations in scalar statistics has been developed. In it, a symmetric matrix, the R tensor, is used to represent the local average residual as a function of diffraction geometry. An effective value of the statistic in question can then be found for any direction in reciprocal space. Differences between these effective R indices for individual reflections or groups of reflections can help to steer refinement strategy and assess the final structure.}, affiliation = {Biochemistry Department, Duke University Medical Center, Durham, NC, USA. sparkin_at_pop.uky.edu}, } @ARTICLE{Parkin98, author = {S. Parkin and H. Hope}, title = {Macromolecular cryocrystallography: Cooling, mounting, storage and transportation of crystals}, journal = {J Appl Cryst}, year = {1998}, volume = {31}, pages = {945-53}, } @ARTICLE{Perrakis99, author = {A Perrakis and R Morris and VS Lamzin}, title = {Automated protein model building combined with iterative structure refinement.}, journal = {Nat Struct Biol}, year = {1999}, volume = {6}, number = {5}, pages = {458-63}, month = {May}, doi = {10.1038/8263}, owner = {miguel}, abstract = {In protein crystallography, much time and effort are often required to trace an initial model from an interpretable electron density map and to refine it until it best agrees with the crystallographic data. Here, we present a method to build and refine a protein model automatically and without user intervention, starting from diffraction data extending to resolution higher than 2.3 A and reasonable estimates of crystallographic phases. The method is based on an iterative procedure that describes the electron density map as a set of unconnected atoms and then searches for protein-like patterns. Automatic pattern recognition (model building) combined with refinement, allows a structural model to be obtained reliably within a few CPU hours. We demonstrate the power of the method with examples of a few recently solved structures.}, keywords = {Adaptor Protein Complex alpha Subunits, Adaptor Proteins, Algorithms, Animals, Automation, Carbon-Nitrogen Lyases, Chitinase, Crystallography, X-Ray, Electrons, GroEL Protein, Ligases, Mannosidases, Membrane Proteins, Metalloendopeptidases, Models, Molecular, Pattern Recognition, Protein Conformation, Proteins, Time Factors, beta-Mannosidase, 10331874}, url = {http://dx.doi.org/10.1038/8263}, } @ARTICLE{Powell99, author = {H. R. Powell}, title = {The Rossmann Fourier autoindexing algorithm in MOSFLM.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1690-5}, month = {October}, abstract = {The fast Fourier transform (FFT) autoindexing routines written by the Rossmann group at Purdue University have been incorporated in MOSFLM, providing a rapid and reliable method of indexing oscillation images. This is a procedure which extracts direct-space information about the unit cell from the FFT. The method and its implementation in MOSFLM are discussed.}, keywords = {Algorithms Crystallography, X-Ray/*methods *Fourier Analysis Internet Nerve Tissue Proteins/chemistry Software Support, Non-U.S. Gov't src Homology Domains}, affiliation = {MRC-LMB, MRC Centre, Hills Road, Cambridge CB2 2QU, England. harry_at_mrc-lmb.cam.ac.uk}, } @ARTICLE{Provost91, author = {K. Provost and M. C. Robert}, title = {Application of gel growth to hanging drop technique}, journal = {Journal of Crystal Growth}, year = {1991}, volume = {110}, pages = {258-64}, } @ARTICLE{Read86, author = {R. J. Read}, title = {Improved fourier coefficients for maps using phases from partial structures with errors}, journal = {Acta Cryst A}, year = {1986}, volume = {42}, pages = {140-9}, } @ARTICLE{Read90, author = {R. J. Read}, title = {Structure factor probabilities for related structures}, journal = {Acta Cryst A}, year = {1990}, volume = {46}, pages = {900-12}, } @ARTICLE{Redinbo93, author = {M. R. Redinbo and T. O. Yeats}, title = {Structure determination of plastocyanin from a specimen with a hemihedral twinning fraction of one-half}, journal = {Acta Cryst D}, year = {1993}, volume = {49}, pages = {375-80}, } @ARTICLE{Riboldi99, author = {A. Riboldi-Tunnicliffe and R. Hilgenfeld}, title = {Cryocrystallography with oil - an old idea revived}, journal = {J Appl Cryst}, year = {1999}, volume = {32}, pages = {1003-5}, } @ARTICLE{Roberts95, author = {A. L. U. Roberts and A. T. Brünger}, title = {Phase improvement by cross-validated density modification}, journal = {Acta Cryst D}, year = {1995}, volume = {51}, pages = {990-1002}, } @ARTICLE{Rossmann99, author = {M. G. Rossmann and C. G. van Beek}, title = {Data processing.}, journal = {Acta Cryst D}, year = {1999}, volume = {55 ( Pt 10)}, pages = {1631-40}, month = {October}, abstract = {X-ray diffraction data processing proceeds through indexing, pre-refinement of camera parameters and crystal orientation, intensity integration, post-refinement and scaling. The DENZO program has set new standards for autoindexing, but no publication has appeared which describes the algorithm. In the development of the new Data Processing Suite (DPS), one of the first aims has been the development of an autoindexing procedure at least as powerful as that used by DENZO. The resultant algorithm will be described. Another major problem which has arisen in recent years is scaling and post-refinement of data from different images when there are few, if any, full reflections. This occurs when the mosaic spread approaches or exceeds the angle of oscillation, as is usually the case for frozen crystals. A procedure which is able to obtain satisfactory results for such a situation will be described.}, keywords = {Algorithms *Automatic Data Processing Crystallography, X-Ray/*methods Ferredoxins/chemistry Fourier Analysis Software Support, U.S. Gov't, Non-P.H.S. Viral Proteins/chemistry}, affiliation = {Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA. mgr_at_indiana.bio.purdue.edu}, } @ARTICLE{Sharff00, author = {A. J. Sharff and E. Koronakis and B. Luisi and V. Koronakis}, title = {Oxidation of selenomethionine: some MADness in the method!}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 6)}, pages = {785-8}, month = {June}, abstract = {Since it was first reported, the multiwavelength anomalous diffraction (MAD) technique for the determination of protein structures has become widely accepted and increasingly popular. Here, it is demonstrated that the anomalous signal from selenomethione (SeMet) substituted proteins can be significantly enhanced by oxidation.}, keywords = {*Amino Acid Substitution/genetics Bacterial Outer Membrane Proteins/chemistry/genetics Crystallization Crystallography, X-Ray/*methods Escherichia coli Hydrogen Peroxide/chemistry Mercaptoethanol/chemistry Oxidation-Reduction Recombinant Proteins/chemistry Reducing Agents/chemistry Selenomethionine/*chemistry Support, Non-U.S. Gov't}, affiliation = {Department of Biochemistry, University of Cambridge, England. andrew_at_cryst.bioc.cam.ac.uk}, } @ARTICLE{Sheldrick02, author = {G. M. Sheldrick}, journal = {Z. Kristallogr.}, year = {2002}, volume = {217}, pages = {644-650}, owner = {miguel}, } @INBOOK{Shelxd98, chapter = {SHELX: applications to macromolecules}, pages = {401-11}, title = {Direct methods for solving macromolecular structures}, publisher = {Kluwer Academic Publishers}, year = {1998}, editor = {F. S. Dordrecht}, author = {G. M. Sheldrick}, } @ARTICLE{Shelxl97, author = {G. M. Sheldrick and T. R. Schneider}, title = {SHELXL: High-resolution refinement}, journal = {Methods in Enzymology}, year = {1997}, volume = {277}, pages = {319-43}, } @ARTICLE{Shelxs96, author = {G. M. Sheldrick}, title = {Patterson superposition and \emph{ab initio} methods}, journal = {Methods in Enzymology}, year = {1997}, volume = {276}, pages = {628-41}, } @ARTICLE{Sheriff87, author = {S. Sheriff and W. A. Hendrickson}, title = {Description of overall anisotropy in diffraction from macromolecular crystals}, journal = {Acta Cryst A}, year = {1987}, volume = {43}, pages = {118-21}, } @ARTICLE{Shindyalov98, author = {IN Shindyalov and PE Bourne}, title = {Protein structure alignment by incremental combinatorial extension ({CE}) of the optimal path.}, journal = {Protein Eng}, year = {1998}, volume = {11}, number = {9}, pages = {739-47}, month = {Sep}, abstract = {A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs (AFPs) rather than the more conventional techniques using dynamic programming and Monte Carlo optimization. AFPs, as the name suggests, are pairs of fragments, one from each protein, which confer structure similarity. AFPs are based on local geometry, rather than global features such as orientation of secondary structures and overall topology. Combinations of AFPs that represent possible continuous alignment paths are selectively extended or discarded thereby leading to a single optimal alignment. The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. The method has been tested and compared with results from Dali and VAST using a representative sample of similar structures. Several new structural similarities not detected by these other methods are reported. Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http://cl.sdsc.edu/ce.html.}, owner = {miguel}, keywords = {Algorithms, Amino Acid Sequence, Molecular Sequence Data, Monte Carlo Method, Protein Conformation, Protein Folding, Proteins, Sequence Alignment, Sequence Homology, Amino Acid, Support, U.S. Gov't, Non-P.H.S., 9796821}, } @ARTICLE{Shneerson01, author = {V. L. Shneerson and D. L. Wild and D. K. Saldin}, title = {An exponential modeling algorithm for protein structure completion by X-ray crystallography.}, journal = {Acta Crystallogr A}, year = {2001}, volume = {57}, number = {Pt 2}, pages = {163-75}, month = {March}, abstract = {An exponential modeling algorithm is developed for protein structure completion by X-ray crystallography and tested on experimental data from a 59-residue protein. An initial noisy difference Fourier map of missing residues of up to half of the protein is transformed by the algorithm into one that allows easy identification of the continuous tube of electron density associated with that polypeptide chain. The method incorporates the paradigm of phase hypothesis generation and cross validation within an automated scheme.}, keywords = {Algorithms Crystallography, X-Ray Elapid Venoms/chemistry Fourier Analysis Models, Molecular Protein Conformation Proteins/*chemistry Support, U.S. Gov't, Non-P.H.S.}, affiliation = {Department of Physics, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.}, } @ARTICLE{Sica94, author = {F. Sica and D. Demasi and L. Mazzarella and A. Zagari and S. Capasso and L. H. Pearl and S. D'Auria and C. A. Raia and M. Rossi}, title = {Elimination of twinning in crystals of \emph{Sulfobolus solfataricus} alcohol dehydrogenase holo-enzyme by groth in agarose gels}, journal = {Acta Cryst D}, year = {1994}, volume = {50}, pages = {508-11}, } @ARTICLE{Stanley72, author = {E. Stanley}, title = {The identification of twins from intensity statistics}, journal = {J Appl Cryst}, year = {1972}, volume = {5}, pages = {191-4}, } @ARTICLE{Storoni04, author = {Laurent C Storoni and Airlie J McCoy and Randy J Read}, title = {Likelihood-enhanced fast rotation functions.}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {2004}, volume = {60}, number = {Pt 3}, pages = {432-8}, month = {Mar}, pii = {S0907444903028956}, doi = {10.1107/S0907444903028956}, abstract = {Experiences with the molecular-replacement program Beast have shown that maximum-likelihood rotation targets are more sensitive to the correct orientation than traditional targets. However, this comes at a high computational cost: brute-force rotation searches can take hours or even days of computation time on current desktop computers. Series approximations to the full likelihood target have been developed that can be computed by fast Fourier transforms in minutes. These likelihood-enhanced targets are more sensitive to the correct orientation than the Crowther fast rotation function and they take advantage of information from partial solutions. The likelihood-enhanced rotation targets have been implemented in the program Phaser.}, owner = {miguel}, keywords = {14993666}, url = {http://dx.doi.org/10.1107/S0907444903028956}, } @ARTICLE{Stura92, author = {E. A. Stura and G. R. Nemerow and I. A. Wilson}, title = {Strategies in the crystallization of glycoproteins and protein complexes}, journal = {Journal of Crystal Growth}, year = {1992}, volume = {122}, pages = {273-85}, } @ARTICLE{Terwilliger03, author = {Thomas C Terwilliger}, title = {Statistical density modification using local pattern matching.}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {2003}, volume = {59}, number = {Pt 10}, pages = {1688-701}, month = {Oct}, pii = {S0907444903015142}, abstract = {A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using model data and templates calculated at a resolution of 2.6 A. Owing to this independence of errors, information from the new map can be combined in a simple fashion with information from the original map to create an improved map. An iterative phase-improvement process using this approach and other applications of the image-reconstruction method are described and applied to experimental data at resolutions ranging from 2.4 to 2.8 A.}, owner = {miguel}, keywords = {Crystallography, X-Ray, Electrostatics, Image Processing, Computer-Assisted, Models, Molecular, Peptide Initiation Factors, Support, U.S. Gov't, P.H.S., Viral Proteins, 14501107}, } @ARTICLE{Tickle00, author = {I. J. Tickle and R. A. Laskowski and D. S. Moss}, title = {Rfree and the rfree ratio. II. Calculation of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement.}, journal = {Acta Cryst D}, year = {1998}, volume = {56}, pages = {442-50}, month = {Apr 1}, keywords = {*Algorithms Crystallography, X-Ray/*methods *Least-Squares Analysis Molecular Structure}, affiliation = {Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, England.}, } @ARTICLE{Tickle98, author = {I. J. Tickle and R. A. Laskowski and D. S. Moss}, title = {Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of gammaB- and betaB2-crystallin.}, journal = {Acta Cryst D}, year = {1998}, volume = {54 ( Pt 2)}, pages = {243-52}, month = {Mar 1}, abstract = {Faster workstations with larger memories are making error estimation from full-matrix least-squares refinement a more practicable technique in protein crystallography. Using minimum variance weighting, estimated standard deviations of atomic positions have been calculated for two eye lens proteins from the inverse of a least-squares normal matrix which was full with respect to the coordinate parameters. gammaB-crystallin, refined at 1.49 A yielded average errors in atomic positions which ranged from 0.05 A for main-chain atoms to 0.27 A for unrestrained water molecules. The second structure used in this work was that of betaB2-crystallin refined at 2.1 A resolution where the corresponding average errors were 0.08 and 0.35 A, respectively. The relative errors in atomic positions are dependent on the number and kinds of restraints used in the refinements. It is also shown that minimum variance weighting leads to mean-square deviations from target geometry in the refined structures which are smaller than the variances used in the distance weighting.}, keywords = {Animal Biometry Crystallins/*chemistry Crystallography, X-Ray/*methods Data Interpretation, Statistical Least-Squares Analysis Models, Statistical}, affiliation = {Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, England.}, } @ARTICLE{Tickle98a, author = {I. J. Tickle and R. A. Laskowski and D. S. Moss}, title = {Rfree and the rfree ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement.}, journal = {Acta Cryst D}, year = {1998}, volume = {54 ( Pt 4)}, pages = {547-57}, month = {Jul 1}, abstract = {The last five years have seen a large increase in the use of cross validation in the refinement of macromolecular structures using X-ray data. In this technique a test set of reflections is set aside from the working set and the progress of the refinement is monitored by the calculation of a free R factor which is based only on the excluded reflections. This paper gives estimates for the ratio of the free R factor to the R factor calculated from the working set for both unrestrained and restrained refinement. It is assumed that both the X-ray and restraint observations have been weighted correctly and that there is no correlation of errors between the test and working sets. It is also shown that the least-squares weights that minimize the variances of the refined parameters, also approximately minimize the free R factor. The estimated free R-factor ratios are compared with those reported for structures in the Protein Data Bank.}, keywords = {*Algorithms Crystallography, X-Ray/*methods *Least-Squares Analysis Molecular Structure}, affiliation = {Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, England.}, } @ARTICLE{Tronrud87, author = {D. E. Tronrud and L. F. Ten Eyck and B. W. Matthews}, title = {An efficient general-purpose least-squares refinement program for macromolecular structures}, journal = {Acta Cryst A}, year = {1987}, volume = {43}, pages = {489-501}, } @ARTICLE{Tronrud92, author = {D. E. Tronrud}, title = {Conjugate-direction minimization: an improved method for the refinement of macromolecules}, journal = {Acta Cryst A}, year = {1992}, volume = {48}, pages = {912-6}, } @ARTICLE{Uson99, author = {I Usón and GM Sheldrick}, title = {Advances in direct methods for protein crystallography.}, journal = {Curr Opin Struct Biol}, year = {1999}, volume = {9}, number = {5}, pages = {643-8}, month = {Oct}, pii = {sb9508}, abstract = {Recent advances in ab initio direct methods have enabled the solution of crystal structures of small proteins from native X-ray data alone, that is, without the use of fragments of known structure or the need to prepare heavy-atom or selenomethionine derivatives, provided that the data are available to atomic resolution. These methods are also proving to be useful for locating the selenium atoms or other anomalous scatterers in the multiple wavelength anomalous diffraction phasing of larger proteins at lower resolution.}, owner = {miguel}, keywords = {Animals, Crystallography, X-Ray, Invertebrate Hormones, Models, Molecular, Protein Conformation, Proteins, 10508770}, } @ARTICLE{Verschueren99, author = {K. H. Verschueren and R. Tyrrell and G. N. Murshudov and E. J. Dodson and A. J. Wilkinson}, title = {Solution of the structure of the cofactor-binding fragment of CysB: a struggle against non-isomorphism.}, journal = {Acta Crystallogr D Biol Crystallogr}, year = {1999}, volume = {55 ( Pt 2)}, pages = {369-78}, month = {February}, abstract = {The elucidation of the structure of CysB(88-324) by multiple isomorphous replacement (MIR) techniques was seriously delayed by problems encountered at every stage of the analysis. There was extensive non-isomorphism both between different native crystals and between native and heavy-atom-soaked crystals. The heavy-atom substitution was invariably weak and different soaking experiments frequently led to substitution at common sites. These correlated heavy-atom binding sites resulted in an overestimation of the phase information. Missing low-resolution reflections in the native data set, constituting only 2\% of the total observations, reduced the power of density modification and phase refinement. Finally, the extensive dimer interface made it difficult to isolate a single molecule in the course of model building into the MIR maps. The power of maximum likelihood refinement (REFMAC) was exploited in solving the structure by means of iterative cycles of refinement of a partial model, initially comprising only 30\% of the protein atoms in the final coordinate set. This technique, which uses experimental phases, can automatically discriminate the correct and incorrect parts of electron-density maps and give properly weighted combined phases which are better than the experimental or calculated ones. This allowed the model to be gradually extended by manual building into improved electron-density maps. A model generated in this way, containing just 50\% of the protein atoms, proved good enough to find the transformations needed for multi-crystal averaging between different crystal forms. The averaging regime im-proved the phasing dramatically such that the complete model could be built. The problems, final solutions and some possible causes for the observed lack of isomorphism are discussed.}, keywords = {Bacterial Proteins/*chemistry Evaluation Studies Models, Molecular Peptide Fragments/*chemistry/metabolism Protein Binding Protein Conformation Support, Non-U.S. Gov't}, affiliation = {Protein Structure Research Group, Department of Chemistry, University of York, Heslington, York YO1 5DD, England. koen_at_yorvic.york.ac.uk}, } @ARTICLE{VonDreele00, author = {Von Dreele, R. B. and P. W. Stephens and G. D. Smith and R. H. Blessing}, title = {The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding.}, journal = {Acta Cryst D}, year = {2000}, volume = {56 Pt 12}, pages = {1549-53}, month = {December}, abstract = {X-ray diffraction analysis of protein structure is often limited by the availability of suitable crystals. However, the absence of single crystals need not present an insurmountable obstacle in protein crystallography any more than it does in materials science, where powder diffraction techniques have developed to the point where complex oxide, zeolite and small organic molecular structures can often be solved from powder data alone. Here, that fact is demonstrated with the structure solution and refinement of a new variant of the T(3)R(3) Zn-human insulin complex produced by mechanical grinding of a polycrystalline sample. High-resolution synchrotron X-ray powder diffraction data were used to solve this crystal structure by molecular replacement adapted for Rietveld refinement. A complete Rietveld refinement of the 1630-atom protein was achieved by combining 7981 stereochemical restraints with a 4800-step (d(min) = 3.24 A) powder diffraction pattern and yielded the residuals R(wp) = 3.73\%, R(p) = 2.84\%, R(F)(2) = 8.25\%. It was determined that the grinding-induced phase change is accompanied by 9.5 and 17.2 degrees rotations of the two T(3)R(3) complexes that comprise the crystal structure. The material reverts over 2-3 d to recover the original T(3)R(3) crystal structure. A Rietveld refinement of this 815-atom protein by combining 3886 stereochemical restraints with a 6000-step (d(min) = 3.06 A) powder diffraction pattern yielded the residuals R(wp) = 3.46\%, R(p) = 2.64\%, R(F)(2) = 7.10\%. The demonstrated ability to solve and refine a protein crystal structure from powder diffraction data suggests that this approach can be employed, for example, to examine structural changes in a series of protein derivatives in which the structure of one member is known from a single-crystal study.}, keywords = {Human Insulin/*chemistry Models, Molecular Polymers/chemistry Protein Conformation Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. X-Ray Diffraction Zinc/*chemistry}, affiliation = {Manuel Lujan Jr Neutron Scattering Center, MS H805, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. vondreele_at_lanl.gov}, } @ARTICLE{Walker98, author = {L. Walker and P. O. Moreno and H. Hope}, title = {Cryocrystallography: effect of cooling medium on sample cooling rate}, journal = {J Appl Cryst}, year = {1998}, volume = {31}, pages = {954-6}, } @ARTICLE{Winn01, author = {M. D. Winn and M. N. Isupov and G. N. Murshudov}, title = {Use of TLS parameters to model anisotropic displacements in macromolecular refinement.}, journal = {Acta Cryst D}, year = {2001}, volume = {57}, number = {Pt 1}, pages = {122-33}, month = {January}, abstract = {An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.}, keywords = {Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry *Models, Molecular Protein Conformation Support, Non-U.S. Gov't}, affiliation = {Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England. m.d.winn_at_dl.ac.uk}, } @ARTICLE{Xu00, author = {H. Xu and H. A. Hauptman and C. M. Weeks and R. Miller}, title = {P1 Shake-and-Bake: can success be guaranteed?}, journal = {Acta Cryst D}, year = {2000}, volume = {56 ( Pt 2)}, pages = {238-40}, month = {February}, abstract = {The multi-trial direct-methods procedure known as Shake-and-Bake has been applied to three small proteins (alpha-1 peptide, vancomycin and lysozyme) that crystallize in space group P1. Phase refinement was accomplished through parameter-shift optimization using both the cosine and exponential forms of the minimal function. By extending error-free data to sufficiently high resolution, 100\% convergence of trial structures to solution could be achieved in all three cases by using the exponential minimal function and a shift angle in the range 130-150 degrees. These results suggest optimum parameters for other P1 structures and emphasize the importance of collecting data to the highest possible resolution.}, keywords = {*Algorithms Crystallization Crystallography, X-Ray/*methods Muramidase/chemistry Proteins/*chemistry Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. Vancomycin/chemistry}, affiliation = {Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, NY 14203, USA. xu_at_hwi.buffalo.edu}, } @ARTICLE{Yu99, author = {B. Yu and M. Blaber and A. M. Gronenborn and G. M. Clore and D. L. Caspar}, title = {Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.}, journal = {Proc Natl Acad Sci U S A}, year = {1999}, volume = {96}, number = {1}, pages = {103-8}, month = {Jan 5}, abstract = {Water in the hydrophobic cavity of human interleukin 1beta, which was detected by NMR spectroscopy but was invisible by high resolution x-ray crystallography, has been mapped quantitatively by measurement and phasing of all of the low resolution x-ray diffraction data from a single crystal. Phases for the low resolution data were refined by iterative density modification of an initial flat solvent model outside the envelope of the atomic model. The refinement was restrained by the condition that the map of the difference between the electron density distribution in the full unit cell and that of the atomic model be flat within the envelope of the well ordered protein structure. Care was taken to avoid overfitting the diffraction data by maintaining phases for the high resolution data from the atomic model and by a resolution-dependent damping of the structure factor differences between data and model. The cavity region in the protein could accommodate up to four water molecules. The refined solvent difference map indicates that there are about two water molecules in the cavity region. This map is compatible with an atomic model of the water distribution refined by using XPLOR. About 70\% of the time, there appears to be a water dimer in the central hydrophobic cavity, which is connected to the outside by two constricted channels occupied by single water molecules approximately 40\% of the time on one side and approximately 10\% on the other.}, keywords = {Computer Simulation Crystallography, X-Ray/*methods Electrons Human Interleukin-1/*chemistry Models, Molecular Software Support, U.S. Gov't, P.H.S. Water/*chemistry}, affiliation = {Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.}, } @ARTICLE{Zeppezauer68, author = {M. Zeppezauer and H. Eklund and E. S. Zeppezauer}, title = {Micro diffusion cells for the growth of single protein crystals by means of equilibrium dialysis.}, journal = {Arch Biochem Biophys}, year = {1968}, volume = {126}, number = {2}, pages = {564-73}, month = {August}, keywords = {Alcohol Oxidoreductases/analysis Animal Arthrobacter/enzymology Crystallography/*instrumentation Dialysis Diffusion Fructose-Bisphosphate Aldolase/analysis Liver/enzymology Microchemistry Muramidase/analysis Muscles/enzymology Peptide Hydrolases/analysis Proteins/*analysis}, }