PARVATI analysis of 3chb Wed Sep 16 13:52:35 2009
Parvati version 2.7eam

Notes

Anisotropy is defined as the ratio of the minimum and maximum Eigenvalues of the 3x3 matrix of anisotropic displacement parameters (ADPs). This is the square of the axial ratio of an ellipsoid representing the atom. The ratio is 1.0 for a perfectly isotropic (spherical) atom. As the ratio decreases from 1.0 to 0.0, it describes an increasingly non-spherical atom, either a 'pancake' or a 'cigar'. The figure to the right shows a typical distribution of anisotropy, with mean 0.45 and standard deviation 0.15, based on analysis of structures in the Protein Data Bank [Merritt (1999) Acta Cryst. D55, 1109-1117]. When analyzing a newly-refined protein model for which the distribution of anisotropy is substantially different from the plot shown, you should investigate whether the restraints applied to ADPs during refinement were appropriately weighted.

Since the purpose of the Parvati script is to analyze anisotropy, atoms which are perfectly isotropic are not included in the statistical summaries. Atoms with no ANISOU record and atoms whose ADPs describe a perfect sphere are ignored.

A breakdown by atom type is given only if the input PDB file contains the atom type in columns 77:78. This is standard as of 1997, but not all PDB files conform to the standard. Oxygen atoms in residue types HOH, H2O, or WAT are listed as "solvent", and are not included in the breakdown by atom type.

File info

HEADER    TOXIN                                   24-MAR-98   3CHB              
TITLE     CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE           
AUTHOR    E.A.MERRITT,W.G.J.HOL                                                 
REVDAT   3   28-JUL-09 3CHB    1       HET    HETATM                            
REVDAT   2   24-FEB-09 3CHB    1       VERSN                                    
REVDAT   1   12-AUG-98 3CHB    0                                                
REMARK   2 RESOLUTION.    1.25 ANGSTROMS.                                       

************************************************
 Raster3D Thermal Ellipsoid Program V2.7EAM 
 E A Merritt -  03 Sep 2009
************************************************

Errors

 ... no errors found in input file

Checking for neighboring atoms with dissimilar Uij (Suv < 0.975)... 

 GLU E  36         MET E  37     CCuij =   0.9478
  CG1A ILE E__74          CD1B ILE E__74     Suv =   0.9737
  CG   ASP H__59          OD2  ASP H__59     Suv =   0.9714

Extreme Anisotropy (axis ratio < 1:10)

 Atom    Residue     Principle axes       Anisotropy    Uiso
_____ __________  ____________________    __________  ______

   C3 GAL D__104  0.2137 0.1244 0.0167        0.0783  0.1183

Large Anisotropy (axis ratio < 1:5)

 Atom    Residue     Principle axes       Anisotropy    Uiso
_____ __________  ____________________    __________  ______

    O ASN G___44  0.6556 0.1607 0.0798        0.1218  0.2988
    O HOH H_9468  0.9092 0.2470 0.1179        0.1296  0.4247
 CD1B ILE H___74  0.1393 0.1182 0.0188        0.1353  0.0921
 CD1B ILE D___74  0.1641 0.1087 0.0235        0.1432  0.0987
    O HOH D_9322  0.8159 0.3222 0.1199        0.1469  0.4193
  OE2 GLU D___83  0.5824 0.2142 0.0894        0.1535  0.2954
   O2 GAL F__104  0.4531 0.1656 0.0732        0.1614  0.2306
   CB GLU F___29  0.4399 0.2023 0.0729        0.1657  0.2384
   CD ARG D___73  0.2206 0.1443 0.0370        0.1678  0.1340
   CG GLU D___29  0.3377 0.1530 0.0571        0.1691  0.1826
  OD2 ASP E___70  0.5663 0.2901 0.0971        0.1716  0.3178
  NH1 ARG E___94  0.7557 0.3862 0.1303        0.1724  0.4240
   CB LYS G___43  0.3965 0.1819 0.0724        0.1825  0.2170
  OE2 GLU G___79  0.7280 0.4444 0.1375        0.1888  0.4366
    O ASN E___44  0.6961 0.2590 0.1323        0.1901  0.3625
  OG1 THR F___15  0.6179 0.2133 0.1182        0.1913  0.3164
   NZ LYS G___62  0.7371 0.5941 0.1426        0.1935  0.4913
  ND2 ASN F____4  0.5351 0.2127 0.1042        0.1947  0.2840
  ND2 ASN G___14  0.2733 0.2453 0.0534        0.1956  0.1907
  NH2 ARG H___67  0.3797 0.1833 0.0746        0.1965  0.2125
   NZ LYS G___84  0.7581 0.2377 0.1499        0.1977  0.3819
    O HOH H_9366  0.6464 0.2217 0.1280        0.1980  0.3321
  NH1 ARG E___73  0.5249 0.1799 0.1049        0.1998  0.2699

Rogues Gallery


ASN G 44
ILE H 74
ILE D 74
GLU D 83
GLU F 29
ARG D 73

GLU D 29
ASP E 70
ARG E 94
LYS G 43
GLU G 79
These are rastep figures of the protein residues containing the most severely anisotropic atoms. Although large anisotropy does not by itself indicate a problem in the refined model, you should inspect these residues to make sure that it makes sense in the context of the surrounding atoms. At most 12 residues are shown. Residues are not selected for the Rogues gallery simply because they contain an atom whose ADP descriptors have gone non-positive definite (you have 0 of these). However, if you are so unfortunate as to have such atoms in residues selected for other reasons, they will appear as ghostly purple shapes.

Distribution of anisotropy by atom class

protein atoms

# Anisotropy  Fraction   Number
#   range     of atoms of atoms
 0.00 0.05      0.000         0
 0.05 0.10      0.000         0
 0.10 0.15      0.001         3
 0.15 0.20      0.004        16
 0.20 0.25      0.020        80
 0.25 0.30      0.039       160
 0.30 0.35      0.068       278
 0.35 0.40      0.116       474
 0.40 0.45      0.151       620
 0.45 0.50      0.166       682
 0.50 0.55      0.153       629
 0.55 0.60      0.121       496
 0.60 0.65      0.079       323
 0.65 0.70      0.043       175
 0.70 0.75      0.024        97
 0.75 0.80      0.011        46
 0.80 0.85      0.003        14
 0.85 0.90      0.001         5
 0.90 0.95      0.000         0
 0.95 1.00      0.000         0
#
#  number of ANISOU records:      4098
#       non-isotropic atoms:      4098
#           isotropic atoms:         0
#
# correlation of anisotropy with B_iso: -0.354
#
#              Anisotropy  B_iso
#  AtomType   mean  sigma   mean  number
# ---------   ----------- ------  ------
#|    Total  0.483  0.119  14.21    4098

solvent atoms

# Anisotropy  Fraction   Number
#   range     of atoms of atoms
 0.00 0.05      0.000         0
 0.05 0.10      0.000         0
 0.10 0.15      0.003         2
 0.15 0.20      0.001         1
 0.20 0.25      0.020        15
 0.25 0.30      0.033        25
 0.30 0.35      0.086        65
 0.35 0.40      0.142       108
 0.40 0.45      0.135       102
 0.45 0.50      0.135       102
 0.50 0.55      0.131        99
 0.55 0.60      0.121        92
 0.60 0.65      0.080        61
 0.65 0.70      0.053        40
 0.70 0.75      0.038        29
 0.75 0.80      0.016        12
 0.80 0.85      0.005         4
 0.85 0.90      0.001         1
 0.90 0.95      0.000         0
 0.95 1.00      0.000         0
#
#  number of ANISOU records:       758
#       non-isotropic atoms:       758
#           isotropic atoms:         0
#
# correlation of anisotropy with B_iso:  0.111
#
#              Anisotropy  B_iso
#  AtomType   mean  sigma   mean  number
# ---------   ----------- ------  ------
#|    Total  0.486  0.128  26.61     758

non-solvent HETATMs

# Anisotropy  Fraction   Number
#   range     of atoms of atoms
 0.00 0.05      0.000         0
 0.05 0.10      0.003         1
 0.10 0.15      0.000         0
 0.15 0.20      0.003         1
 0.20 0.25      0.017         6
 0.25 0.30      0.032        11
 0.30 0.35      0.040        14
 0.35 0.40      0.046        16
 0.40 0.45      0.124        43
 0.45 0.50      0.130        45
 0.50 0.55      0.118        41
 0.55 0.60      0.098        34
 0.60 0.65      0.104        36
 0.65 0.70      0.110        38
 0.70 0.75      0.069        24
 0.75 0.80      0.058        20
 0.80 0.85      0.029        10
 0.85 0.90      0.009         3
 0.90 0.95      0.012         4
 0.95 1.00      0.000         0
#
#  number of ANISOU records:       347
#       non-isotropic atoms:       347
#           isotropic atoms:         0
#
# correlation of anisotropy with B_iso:  0.252
#
#              Anisotropy  B_iso
#  AtomType   mean  sigma   mean  number
# ---------   ----------- ------  ------
#|    Total  0.552  0.152  22.62     347

Agreement of ellipsoids across peptide C-N bond


This plot highlights bad joins between TLS groups. A bad join is one where the C and N atoms of the bond linking two TLS groups have very different ADPs (thermal ellipsoids). If the atoms are similar, their correlation coefficient CCuij is near 1. If there is a bad join, it will show at as a downward spike in CCuij at that point. There is nothing magic about the threshold 0.9. We picked it because 95% of the structures we sampled from the PDB refined with TLS do not trigger this threshold. Of the remaining 5%, many are probably OK but there are also cases where something has clearly gone wrong.

Mean anisotropy of mainchain atoms


This plot includes atoms labeled C CA N and O.

Mean Beq of mainchain atoms


This plot includes atoms labeled C CA N and O.

Distribution of anisotropy by atom class

3chb Summary

  Anisotropy # atoms
MeanSigma
Protein 0.483 0.119 4098
Solvent 0.486 0.128 758
Hetatms 0.552 0.152 347
Total 0.488 0.124 5203
N 0.471 0.128 729
C 0.497 0.121 2756
O 0.476 0.126 923
S 0.526 0.099 32
X 0.397 0.091 5
  
Click for larger image 
   0 atoms ( 0.0%) with non-positive definite ADPs
   1 atoms ( 0.0%) with anisotropy < 0.10         
  24 atoms ( 0.5%) with anisotropy < 0.20         
   0 atoms in the protein are perfectly isotropic 
   2 pairs of neighboring atoms have S(u,v) < 0.975 
   1 C-N linkages had correlation < 0.950