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
R0.19100.19240.17340.1727
R-free0.24000.23710.21610.2130
σR-free 0.00590.00530.0053
Z(R-free) -0.15-0.60-0.19

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.2240.2270.252
2nd generation packing quality1-1.144-0.964-0.860
Ramachandran plot appearance10.0250.4110.313
Chi-1/Chi-2 rotamer normality1-2.739-1.701-1.562
Backbone conformation10.5700.6740.648
Bond length RMS Z-score20.7130.6760.670
Bond angle RMS Z-score20.7690.8150.809
Total number of bumps3341412
Unsatisfied H-bond donors/acceptors31279
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 residues65
Significantly deteriorated residues0
Changes of all residuesPlot

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