Optimised PDB entry 3pdo



Structure
SpacegroupP 21 21 21
Cell dimensionsa: 45.450 Åb: 97.627 Åc: 99.052 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution1.95 Å

Experimental data
ReflectionsAll: 32809Test set: 1641 (5.0%)
Resolution range33.26 Å1.95 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19100.19230.17340.1728
R-free0.24000.23730.21580.2128
σR-free 0.00590.00530.0053
Z(R-free) -0.20-0.55-0.11

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.2890.2800.334
2nd generation packing quality1-0.880-0.645-0.581
Ramachandran plot appearance10.1100.5490.369
Chi-1/Chi-2 rotamer normality1-2.713-1.581-1.637
Backbone conformation10.8730.9820.962
Bond length RMS Z-score20.7130.6690.665
Bond angle RMS Z-score20.7690.8050.801
Total number of bumps3341617
Unsatisfied H-bond donors/acceptors313119
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 residues54
Significantly deteriorated residues0
Changes of all residuesPlot

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