Optimised PDB entry 3zmi



Structure
SpacegroupH 3 2
Cell dimensionsa: 110.580 Åb: 110.580 Åc: 128.530 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.20 Å

Experimental data
ReflectionsAll: 15409Test set: 777 (5.0%)
Resolution range44.87 Å2.20 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.21650.22100.18840.1857
R-free0.26090.26910.23570.2324
σR-free 0.00970.00850.0083
Z(R-free) -0.19-0.92-0.94

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-1.037-0.981-1.142
2nd generation packing quality1-1.157-0.766-0.804
Ramachandran plot appearance1-2.350-1.823-1.672
Chi-1/Chi-2 rotamer normality1-2.494-2.082-2.185
Backbone conformation1-1.421-1.422-1.405
Bond length RMS Z-score20.3660.6920.682
Bond angle RMS Z-score20.5510.7620.761
Total number of bumps3334
Unsatisfied H-bond donors/acceptors39810
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 residues49
Significantly deteriorated residues0
Changes of all residuesPlot

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