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
R0.17300.17320.15780.1628
R-free0.21700.21200.19370.1960
σR-free 0.00680.00620.0063
Z(R-free) 1.040.951.57

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.282-0.233-0.210
2nd generation packing quality1-0.940-0.978-0.865
Ramachandran plot appearance1-0.837-0.477-0.413
Chi-1/Chi-2 rotamer normality1-1.338-0.523-0.279
Backbone conformation10.1730.2380.253
Bond length RMS Z-score20.7050.5790.583
Bond angle RMS Z-score20.7520.7600.757
Total number of bumps3301718
Unsatisfied H-bond donors/acceptors3261213
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 residues15
Significantly deteriorated residues0
Changes of all residuesPlot

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