Optimised PDB entry 1qdl



Structure
SpacegroupP 63 2 2
Cell dimensionsa: 162.000 Åb: 162.000 Åc: 212.350 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.50 Å

Experimental data
ReflectionsAll: 57117Test set: 2887 (5.1%)
Resolution range29.65 Å2.50 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.22600.22170.18770.1886
R-free0.25400.24240.21000.2065
σR-free 0.00450.00390.0038
Z(R-free) 5.073.725.03

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.3540.4070.417
2nd generation packing quality1-0.720-0.323-0.213
Ramachandran plot appearance1-2.856-0.912-0.769
Chi-1/Chi-2 rotamer normality1-6.964-2.626-1.762
Backbone conformation1-0.296-0.039-0.058
Bond length RMS Z-score20.3620.4640.405
Bond angle RMS Z-score20.6620.7300.655
Total number of bumps3782219
Unsatisfied H-bond donors/acceptors3423641
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 residues241
Significantly deteriorated residues0
Changes of all residuesPlot

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