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
R0.18700.25830.26250.2589
R-free0.27500.32150.31250.3149
σR-free 0.01190.01160.0116
Z(R-free) -1.030.16-0.41

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.598-0.794-0.725
2nd generation packing quality1-0.800-0.920-0.655
Ramachandran plot appearance1-2.876-2.320-2.088
Chi-1/Chi-2 rotamer normality1-6.023-3.978-3.905
Backbone conformation1-0.1660.1170.292
Bond length RMS Z-score20.4340.3820.378
Bond angle RMS Z-score20.7010.6380.626
Total number of bumps3843734
Unsatisfied H-bond donors/acceptors3665957
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 residues1
Significantly deteriorated residues57
Changes of all residuesPlot

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