Optimised PDB entry 1dku



Warnings!

Structure
SpacegroupP 63
Cell dimensionsa: 115.650 Åb: 115.650 Åc: 106.410 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.20 Å

Experimental data
ReflectionsAll: 50000Test set: 0 (0.0%)
Resolution range22.98 Å1.70 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19800.23720.13520.1362
R-free0.24100.23900.17180.1712
σR-free 0.00520.00450.0045
Z(R-free) 10.881.762.18

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.0210.1250.114
2nd generation packing quality1-1.193-0.891-0.765
Ramachandran plot appearance1-1.848-0.395-0.477
Chi-1/Chi-2 rotamer normality1-2.731-1.161-0.438
Backbone conformation1-0.554-0.526-0.593
Bond length RMS Z-score20.7020.5670.567
Bond angle RMS Z-score20.8640.7520.754
Total number of bumps3812822
Unsatisfied H-bond donors/acceptors3373838
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 residues306
Significantly deteriorated residues1
Changes of all residuesPlot

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