Optimised PDB entry 2dfk



Structure
SpacegroupP 21 21 21
Cell dimensionsa: 57.957 Åb: 147.499 Åc: 167.220 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.15 Å

Experimental data
ReflectionsAll: 78688Test set: 3915 (5.0%)
Resolution range45.57 Å2.11 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.18000.18180.17190.1726
R-free0.22900.22960.21290.2142
σR-free 0.00370.00340.0034
Z(R-free) -0.540.680.53

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.2870.6050.660
2nd generation packing quality1-1.016-0.608-0.331
Ramachandran plot appearance1-0.9280.7560.865
Chi-1/Chi-2 rotamer normality1-4.491-2.468-1.610
Backbone conformation1-0.447-0.255-0.284
Bond length RMS Z-score20.9050.5530.549
Bond angle RMS Z-score20.9530.7930.762
Total number of bumps3855247
Unsatisfied H-bond donors/acceptors3495240
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 residues86
Significantly deteriorated residues21
Changes of all residuesPlot

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