Optimised PDB entry 4rdu



Structure
SpacegroupP 1
Cell dimensionsa: 34.182 Åb: 42.913 Åc: 56.104 Å
α: 84.13°β: 77.33°γ: 67.13°
Resolution1.85 Å

Experimental data
ReflectionsAll: 23315Test set: 1188 (5.1%)
Resolution range22.30 Å1.85 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.18300.18430.18190.1865
R-free0.22500.22340.20780.2160
σR-free 0.00650.00600.0063
Z(R-free) 0.222.331.83

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.387-0.2360.166
2nd generation packing quality1-1.048-0.864-0.722
Ramachandran plot appearance12.0333.3833.414
Chi-1/Chi-2 rotamer normality10.2441.6961.272
Backbone conformation1-0.0860.1410.150
Bond length RMS Z-score20.5850.7700.768
Bond angle RMS Z-score20.7500.8920.883
Total number of bumps3353635
Unsatisfied H-bond donors/acceptors3133
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 residues4
Significantly deteriorated residues4
Changes of all residuesPlot

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