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
R0.19000.18810.18670.1859
R-free0.23300.23060.21570.2143
σR-free 0.00440.00410.0041
Z(R-free) 1.344.634.73

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.1830.1710.222
2nd generation packing quality1-1.378-1.177-1.146
Ramachandran plot appearance1-1.352-1.064-1.029
Chi-1/Chi-2 rotamer normality1-1.872-0.910-0.524
Backbone conformation12.0302.1382.142
Bond length RMS Z-score20.6540.4780.476
Bond angle RMS Z-score20.7190.7240.705
Total number of bumps3764843
Unsatisfied H-bond donors/acceptors304242
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 residues8
Changes of all residuesPlot

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