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PDBsum entry 1jdb
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Top Page protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1jdb
Contents
Protein chains
1057 a.a. *
379 a.a. *
Ligands
PO4 ×9
GLN ×8
ADP ×8
ORN ×4
NET ×4
Metals
_CL ×29
_MN ×16
__K ×29
Waters ×4857
* Residue conservation analysis
procheck   Generate full PROCHECK analyses

PROCHECK summary for 1jdb

Ramachandran plot

PROCHECK statistics

1. Ramachandran Plot statistics


                                         No. of
                                        residues     %-tage
                                         ------      ------
Most favoured regions      [A,B,L]         4563       91.1%          
Additional allowed regions [a,b,l,p]        436        8.7%          
Generously allowed regions [~a,~b,~l,~p]      7        0.1%          
Disallowed regions         [XX]               5        0.1%*  
                                           ----      ------
Non-glycine and non-proline residues       5011      100.0%

End-residues (excl. Gly and Pro)             39

Glycine residues                            456
Proline residues                            250
                                           ----
Total number of residues                   5756

Based on an analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20.0 a good quality model would be expected to have over 90% in the most favoured regions [A,B,L].

2. G-Factors

                                                Average
Parameter                            Score       Score
---------                            -----       -----
Dihedral angles:-
     Phi-psi distribution            -0.19      
     Chi1-chi2 distribution          -0.41      
     Chi1 only                       -0.08      
     Chi3 & chi4                      0.33      
     Omega                            0.48      
                                                   0.05      
                                                  =====
Main-chain covalent forces:-
     Main-chain bond lengths          0.30      
     Main-chain bond angles          -0.67*     
                                                  -0.27      
                                                  =====

     OVERALL AVERAGE                              -0.04      
                                                  =====

G-factors provide a measure of how unusual, or out-of-the-ordinary, a property is. 

Values below -0.5*  - unusual
Values below -1.0** - highly unusual
Important note: The main-chain bond-lengths and bond angles are compared with the Engh & Huber (1991) ideal values derived from small-molecule data. Therefore, structures refined using different restraints may show apparently large deviations from normality.

 

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