Optimised PDB entry 3wd5



Structure
SpacegroupI 21 3
Cell dimensionsa: 161.849 Åb: 161.849 Åc: 161.849 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution3.10 Å

Experimental data
ReflectionsAll: 14578Test set: 733 (5.0%)
Resolution range46.72 Å2.98 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.18700.25770.27620.2737
R-free0.27500.32050.31060.3125
σR-free 0.01190.01150.0116
Z(R-free) -1.001.761.32

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.624-0.696-0.655
2nd generation packing quality1-0.444-0.271-0.044
Ramachandran plot appearance1-3.061-2.082-1.769
Chi-1/Chi-2 rotamer normality1-5.918-3.270-2.916
Backbone conformation10.2130.6080.779
Bond length RMS Z-score20.4340.3720.364
Bond angle RMS Z-score20.7010.6030.590
Total number of bumps3841516
Unsatisfied H-bond donors/acceptors3665956
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 residues0
Significantly deteriorated residues104
Changes of all residuesPlot

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