Optimised PDB entry 4jd8



Structure
SpacegroupP 31 2 1
Cell dimensionsa: 37.550 Åb: 37.550 Åc: 54.371 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution1.16 Å

Experimental data
ReflectionsAll: 15696Test set: 789 (5.0%)
Resolution range32.52 Å1.16 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.13800.15810.12170.1376
R-free0.16200.17890.15590.1713
σR-free 0.00640.00560.0061
Z(R-free) 2.59-0.96-0.20

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1NANANA
2nd generation packing quality1NANANA
Ramachandran plot appearance1NANANA
Chi-1/Chi-2 rotamer normality1NANANA
Backbone conformation1NANANA
Bond length RMS Z-score21.5661.5261.539
Bond angle RMS Z-score21.8161.6051.588
Total number of bumps3766
Unsatisfied H-bond donors/acceptors3000
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 residues18
Significantly deteriorated residues2
Changes of all residuesPlot

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