Optimised PDB entry 3l9j



Structure
SpacegroupP 63 2 2
Cell dimensionsa: 83.905 Åb: 83.905 Åc: 149.172 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.10 Å

Experimental data
ReflectionsAll: 18823Test set: 968 (5.1%)
Resolution range41.95 Å2.10 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.17300.17270.15660.1579
R-free0.21700.21190.19250.1901
σR-free 0.00680.00620.0061
Z(R-free) 0.970.901.57

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.281-0.242-0.214
2nd generation packing quality1-0.593-0.589-0.566
Ramachandran plot appearance1-0.740-0.324-0.298
Chi-1/Chi-2 rotamer normality1-2.244-1.284-0.977
Backbone conformation10.8030.8480.798
Bond length RMS Z-score20.7050.5720.568
Bond angle RMS Z-score20.7520.7550.751
Total number of bumps3151010
Unsatisfied H-bond donors/acceptors3121414
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 residues17
Significantly deteriorated residues1
Changes of all residuesPlot

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