# Structure Quality Analysis for NAME

Analyses performed for user defined residues.
The constraints analysis is based on the following files: NOE distance constraints file. Angular constraints file.
Procheck analysis,RMSD calculation and structure superimposition are based on: User defined residues

NESG ID: | NAME
PDB ID: |
Deposition date: |
Common Name: |
Class: |
Length (a.a.): | 121
Organism: |
SwissProt / TrEMBL ID: |
# models: | 20
Oligomerization: | monomer
Molecular weight: | 13596

Secondary Structure Elements:
alpha helices: 29A-41A, 51A-60A, 65A-75A, 85A-98A, 110A-113A
beta strands:

Total number of restricting constraints per restrained residue: | 18.4
Restricting long range constraints per restrained residue: | 3.1

Distance violations per model
Calculated using sum over r^-6

0.1 - 0.2 Å | 0.2 - 0.5 Å | > 0.5 Å
12.4 | 2.6 | 0

Dihedral angle violations per model

1 - 10 ° | > 10 °
7.25 | 0.45

FIDs deposited in the BMRB? no

RPF Scores

Recall | Precision | F-measure | DP-score
0.945 | 0.942 | 0.944 | 0.699

RMSD | All residues | Ordered residues2 | Selected residues3
All backbone atoms | 9.5 Å | 0.8 Å | 0.8 Å
All heavy atoms | 9.9 Å | 1.3 Å | 1.3 Å

Ramachandran Plot Summary for selected residues3 from Procheck

Most favoured regions | Additionally allowed regions | Generously allowed regions | Disallowed regions
90.6% | 9.3% | 0.1% | 0.0%

Ramachandran Plot Summary for selected residues3 from Richardson Lab's Molprobity

Most favoured regions | Allowed regions | Disallowed regions | View plot View model summary
94.7% | 5.2% | 0.1%

Global quality scores

Program | Verify3D | ProsaII (-ve) | Procheck (phi-psi)3 | Procheck (all)3 | MolProbity Clashscore
-Raw score | 0.27 | 0.52 | 0.06 | -0.16 | 25.33
Z-score1 | -3.05 | -0.54 | 0.55 | -0.95 | -2.82

Generalized linear model RMSD prediction: 1.70

Close Contacts and Deviations from Ideal Geometry (from PDB validation software)

Number of close contacts (within 1.6 Å for H atoms, 2.2 Å for heavy atoms): | 85
RMS deviation for bond angles: | 0.6 °
RMS deviation for bond lengths: | 0.004 Å

1 With respect to mean and standard deviation for a set of 252 X-ray structures < 500 residues, of resolution <= 1.80 Å, R-factor <= 0.25 and R-free <= 0.28; a positive value indicates a 'better' score
2Order residues: 24A-44A,48A-82A,84A-102A,105A-113A
3Selected residues: 24A-44A,48A-82A,84A-102A,105A-113A

RPF Precision Map

Residue Plot of Ramachandran anlysis(based on data from Richardson Lab's Molprobity)

References:
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2. Bowie J U, Luthy R and Eisenberg D, "A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure", Science 253 (1991): 164-169
3. Sippl M J, "Recognition of Errors in Three-Dimensional Structures of Proteins", Proteins 17 (1993): 355-362
4. Sippl M J, "Calculation of Conformation Ensembles from Potentials of Mean Force", J Mol Biol 213 (1990): 859-883
5. Laskowski R Ai et al, "AQUA and PROCHECK_NMR: Programs for checking the quality of proteins structures solved by NMR", J Biomolec NMR 8 (1996): 477-486
6. Laskowski R A et al "PROCHECK: a program to check the stereochemical quality of protein structures" J Appl Cryst, 26 (1993): 283-291
7. Word J M et al, "Exploring steric constrains on protein mutations using MAGE / PROBE", Prot Sci 9 (2000): 2251-2259
8. Word J M et al, "Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation", J Mol Biol 285 (1999): 1735-1747
9. Word J M et al, "Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogens", J Mol Biol 285 (1999): 1711-1733
10. Tejero R and Montelione G T, "PDBStat", unpublished
11. Luthy R, McLachlan A D and Eisenberg D, "Secondary Structure-Based Profiles: Use of Structure-Conserving Scoring Tables in Searching Protein Sequence Databases for Structural Similarities", Proteins 10 (1991): 229-239
12. Richardson D C, Richardson J S, "The kinemage: a tool for scientific communication", Prot Sci 1(1) (1992): 3-9
13. Koradi, R, et al, "MOLMOL: a program for display and analysis of macromolecular structures ", J Mol Graphics 14 (1996): 51-55.
14. Güntert, P, Mumenthaler, C & Wüthrich, K "Torsion angle dynamics for NMR structure calculation with the new program DYANA", J. Mol. Biol 273 (1997): 283-298
15. Lovell S C et al, "Structure validation by Calpha geometry: phi,psi and Cbeta deviation" Proteins (2003) 50: 437-450
16. Kabsch W, Sander C, "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features", Biopolymers (1983) 22: 2577-2637
17. Bagaria, A., Jaravine, V., Huang, Y.J., Montelione, G.T., and Guntert, P. "Protein structure validation by generalized linear model root-mean-square deviation prediction". Protein Sci 21(2012), 229-238.

Analysed by on May-10-2013 using PSVS 1.3