Optimised PDB entry 3les



Structure
SpacegroupP 1
Cell dimensionsa: 37.257 Åb: 49.987 Åc: 57.567 Å
α: 78.03°β: 89.83°γ: 87.57°
Resolution2.77 Å

Experimental data
ReflectionsAll: 8837Test set: 912 (10.3%)
Resolution range48.86 Å2.77 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.22700.23910.23910.2320
R-free0.26000.26930.26930.2892
σR-free 0.0089NA0.0096
Z(R-free) 1.98NA-1.13

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.556-0.555-0.170
2nd generation packing quality1-0.521-0.5220.011
Ramachandran plot appearance1-6.154-6.154-3.077
Chi-1/Chi-2 rotamer normality1-5.276-5.276-4.815
Backbone conformation1-0.252-0.252-0.396
Bond length RMS Z-score20.2040.2040.531
Bond angle RMS Z-score20.4330.4330.745
Total number of bumps3444430
Unsatisfied H-bond donors/acceptors3333335
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 residues69
Significantly deteriorated residues3
Changes of all residuesPlot

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