Optimised PDB entry 4k5d



Structure
SpacegroupP 21 21 21
Cell dimensionsa: 51.957 Åb: 110.933 Åc: 164.384 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.10 Å

Experimental data
ReflectionsAll: 56507Test set: 2786 (4.9%)
Resolution range43.92 Å2.10 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19000.18760.18920.1880
R-free0.23300.22940.21930.2177
σR-free 0.00430.00420.0041
Z(R-free) 1.494.434.54

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.914-0.864-0.836
2nd generation packing quality1-1.429-1.234-1.139
Ramachandran plot appearance1-1.170-0.429-0.416
Chi-1/Chi-2 rotamer normality1-3.010-1.836-1.304
Backbone conformation1-1.734-1.595-1.641
Bond length RMS Z-score20.6540.5190.523
Bond angle RMS Z-score20.7190.7420.733
Total number of bumps3574339
Unsatisfied H-bond donors/acceptors3675957
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 residues7
Significantly deteriorated residues5
Changes of all residuesPlot

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