PDBIHM.org

PDB-IHM

System for Archiving Integrative Structures

Model quality ?

For models with atomic structures, MolProbity analysis is performed. For models with coarse-grained or multi-scale structures, excluded volume analysis is performed.

Standard geometry: bond outliers ?

There are no bond length outliers.
Standard geometry: angle outliers ?

There are no bond angle outliers.
Too-close contacts ?

The following all-atom clashscore is based on a MolProbity analysis. All-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The table below contains clashscores for all atomic models in this entry.

Model ID Clash score Number of clashes
1
2.17
2
2
5.43
5
3
0.00
0
4
2.17
2
5
0.00
0
6
1.09
1
7
2.17
2
8
0.00
0
9
0.00
0
10
0.00
0

There are 12 clashes. The table below contains the detailed list of all clashes based on a MolProbity analysis. Bad clashes are >= 0.4 Angstrom.

Atom 1 Atom 2 Clash(Å) Model ID (Worst) Models (Total)
A:9:LEU:O
A:9:LEU:HD23
0.71
2
1
A:9:LEU:C
A:9:LEU:HD23
0.62
2
1
A:50:LEU:O
A:50:LEU:HD23
0.60
4
4
A:50:LEU:C
A:50:LEU:HD23
0.59
4
5
A:9:LEU:C
A:9:LEU:CD2
0.47
2
1

Torsion angles: Protein backbone ?

In the following table, Ramachandran outliers are listed. The Analysed column shows the number of residues for which the backbone conformation was analysed.

Model ID Analysed Favored Allowed Outliers
1
54
54
0
0
2
54
54
0
0
3
54
54
0
0
4
54
54
0
0
5
54
54
0
0
6
54
53
1
0
7
54
54
0
0
8
54
54
0
0
9
54
54
0
0
10
54
54
0
0

Torsion angles : Protein sidechains ?
In the following table, sidechain rotameric outliers are listed. The Analysed column shows the number of residues for which the sidechain conformation was analysed.

Model ID Analysed Favored Allowed Outliers
1
46
46
0
0
2
46
45
1
0
3
46
46
0
0
4
46
46
0
0
5
46
46
0
0
6
46
45
1
0
7
46
46
0
0
8
46
46
0
0
9
46
46
0
0
10
46
45
1
0