Optimised PDB entry 3pgd



Structure
SpacegroupP 43 21 2
Cell dimensionsa: 94.449 Åb: 94.449 Åc: 275.535 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.72 Å

Experimental data
ReflectionsAll: 34493Test set: 1725 (5.0%)
Resolution range33.52 Å2.72 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19600.20230.19670.1896
R-free0.24200.24580.23210.2338
σR-free 0.00590.00560.0056
Z(R-free) -0.510.70-1.12

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.1290.049-0.001
2nd generation packing quality1-1.077-0.790-0.697
Ramachandran plot appearance1-1.081-0.149-0.137
Chi-1/Chi-2 rotamer normality1-4.375-2.388-2.723
Backbone conformation10.6630.5820.535
Bond length RMS Z-score20.3790.4130.537
Bond angle RMS Z-score20.6000.6660.752
Total number of bumps3782130
Unsatisfied H-bond donors/acceptors3323026
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 residues40
Significantly deteriorated residues2
Changes of all residuesPlot

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