Optimised PDB entry 3dk3



Structure
SpacegroupP 21 21 2
Cell dimensionsa: 106.254 Åb: 131.806 Åc: 56.229 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.02 Å

Experimental data
ReflectionsAll: 52048Test set: 2594 (5.0%)
Resolution range28.43 Å2.02 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.21300.21080.19960.2019
R-free0.24800.24080.22530.2279
σR-free 0.00470.00440.0045
Z(R-free) 2.513.163.11

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.649-0.519-0.481
2nd generation packing quality1-0.120-0.0030.149
Ramachandran plot appearance1-0.0650.2610.231
Chi-1/Chi-2 rotamer normality1-0.8790.246-0.134
Backbone conformation1-0.493-0.669-0.683
Bond length RMS Z-score20.3280.4340.452
Bond angle RMS Z-score20.4760.6580.678
Total number of bumps3131310
Unsatisfied H-bond donors/acceptors312912
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 residues52
Significantly deteriorated residues0
Changes of all residuesPlot

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