# Structure Quality Analysis for NAME

Procheck analysis,RMSD calculation and structure superimposition are based on: all residues

NESG ID: | NAME
PDB ID: |
Deposition date: |
Common Name: |
Class: |
Length (a.a.): | 114
Organism: |
SwissProt / TrEMBL ID: |
Oligomerization: | monomer
Molecular weight: | 12426

Secondary Structure Elements:
alpha helices: 10A-19A, 26A-31A, 39A-49A, 110A-114A
beta strands: 37R-38R, 3U-9U, 56U-62U, 93L-98L, 21G-22G, 88U-89U, 34E-35E, 80G-84G, 70U-74U

Resolution: | 1.800 Å | R-factor: | 0.222 | R-free: | 0.252

Structure Factors deposited in the PDB? no

Ramachandran Plot Summary from Procheck

Most favoured regions | Additionally allowed regions | Generously allowed regions | Disallowed regions
92.9% | 6.1% | 1.0% | 0.0%

Ramachandran Plot Summary from Richardson Lab's Molprobity

Most favoured regions | Allowed regions | Disallowed regions | View plot View model summary
97.3% | 2.7% | 0%

Global quality scores

Program | Verify3D | ProsaII (-ve) | Procheck (phi-psi) | Procheck (all) | MolProbity Clashscore
-Raw score | 0.44 | 0.66 | -0.11 | -0.02 | 11.01
Z-score1 | -0.32 | 0.04 | -0.12 | -0.12 | -0.36

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

Number of close contacts (within 2.2 Å): | 0
RMS deviation for bond angles: | 1.3 °
RMS deviation for bond lengths: | 0.005 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

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-9-2013 using PSVS 1.3