Optimised PDB entry 3pgc



Structure
SpacegroupP 31 2 1
Cell dimensionsa: 138.146 Åb: 138.146 Åc: 104.520 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.66 Å

Experimental data
ReflectionsAll: 33394Test set: 1670 (5.0%)
Resolution range34.54 Å2.66 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19800.20190.19170.1947
R-free0.25000.25000.22880.2328
σR-free 0.00610.00560.0057
Z(R-free) -1.260.210.14

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.1220.1390.191
2nd generation packing quality1-1.183-0.607-0.298
Ramachandran plot appearance1-1.383-0.0340.108
Chi-1/Chi-2 rotamer normality1-4.675-3.114-2.632
Backbone conformation10.8090.7850.914
Bond length RMS Z-score20.3790.6520.547
Bond angle RMS Z-score20.5900.8150.754
Total number of bumps3862424
Unsatisfied H-bond donors/acceptors3383837
LinkLinkLink

1 Higher is better, 2 Should be lower than 1.000, 3 Fewer is better


Density map fit (real-space correlation coefficient)
Significantly improved residues44
Significantly deteriorated residues2
Changes of all residuesPlot

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