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
R0.19000.18820.18640.1873
R-free0.23300.23080.21400.2171
σR-free 0.00440.00410.0041
Z(R-free) 1.324.954.49

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.906-0.842-0.810
2nd generation packing quality1-1.374-1.211-1.135
Ramachandran plot appearance1-0.4430.1680.181
Chi-1/Chi-2 rotamer normality1-1.924-1.136-0.653
Backbone conformation1-0.951-0.870-0.771
Bond length RMS Z-score20.6540.4660.475
Bond angle RMS Z-score20.7190.7190.712
Total number of bumps3764839
Unsatisfied H-bond donors/acceptors3534149
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 residues12
Significantly deteriorated residues10
Changes of all residuesPlot

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