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
R0.19800.23860.13410.1344
R-free0.24100.23420.17020.1749
σR-free 0.00510.00440.0046
Z(R-free) 11.781.820.80

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.0220.1410.122
2nd generation packing quality1-1.491-1.202-1.141
Ramachandran plot appearance1-2.399-0.788-0.746
Chi-1/Chi-2 rotamer normality1-4.051-1.710-1.059
Backbone conformation1-0.813-0.568-0.544
Bond length RMS Z-score20.7020.6020.600
Bond angle RMS Z-score20.8640.7790.767
Total number of bumps3612119
Unsatisfied H-bond donors/acceptors3312924
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 residues332
Significantly deteriorated residues0
Changes of all residuesPlot

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