Optimised PDB entry 4gbx



Structure
SpacegroupP 21 21 21
Cell dimensionsa: 66.167 Åb: 126.032 Åc: 143.107 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution3.00 Å

Experimental data
ReflectionsAll: 24570Test set: 1228 (5.0%)
Resolution range36.99 Å3.00 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19800.21990.21510.2196
R-free0.25000.26380.24990.2668
σR-free 0.00750.00710.0076
Z(R-free) 0.011.15-0.43

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.967-0.731-0.829
2nd generation packing quality1-2.119-1.503-1.714
Ramachandran plot appearance1-2.771-1.713-2.015
Chi-1/Chi-2 rotamer normality1-6.014-3.968-4.264
Backbone conformation10.0040.156-0.073
Bond length RMS Z-score20.4210.4160.434
Bond angle RMS Z-score20.6620.6660.713
Total number of bumps31153657
Unsatisfied H-bond donors/acceptors3736172
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 residues37
Significantly deteriorated residues27
Changes of all residuesPlot

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