Optimised PDB entry 4gkk



Structure
SpacegroupP 41 21 2
Cell dimensionsa: 402.370 Åb: 402.370 Åc: 175.620 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution3.20 Å

Experimental data
ReflectionsAll: 230910Test set: 11793 (5.1%)
Resolution range80.48 Å3.20 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19500.20810.20810.1997
R-free0.23600.24700.24700.2495
σR-free 0.0023NA0.0023
Z(R-free) 1.17NA-4.30

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-2.730-2.727-2.886
2nd generation packing quality1-3.049-3.051-3.222
Ramachandran plot appearance1-4.963-4.960-4.632
Chi-1/Chi-2 rotamer normality1-5.686-5.685-5.126
Backbone conformation1-1.184-1.184-1.305
Bond length RMS Z-score20.7760.7830.466
Bond angle RMS Z-score21.1881.1880.858
Total number of bumps3160416081197
Unsatisfied H-bond donors/acceptors3449449400
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 residues655
Significantly deteriorated residues96
Changes of all residuesPlot

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