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
R0.19800.21970.20510.2115
R-free0.25000.26420.25270.2668
σR-free 0.00750.00720.0076
Z(R-free) -0.08-0.92-1.71

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.961-0.804-0.936
2nd generation packing quality1-2.119-1.744-1.814
Ramachandran plot appearance1-2.677-2.047-2.685
Chi-1/Chi-2 rotamer normality1-6.067-4.603-4.883
Backbone conformation1-0.281-0.263-0.808
Bond length RMS Z-score20.4210.4970.527
Bond angle RMS Z-score20.6620.7450.801
Total number of bumps31086491
Unsatisfied H-bond donors/acceptors3735569
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 residues62
Significantly deteriorated residues20
Changes of all residuesPlot

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