Optimised PDB entry 4jt9



Structure
SpacegroupP 65
Cell dimensionsa: 120.464 Åb: 120.464 Åc: 44.468 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.24 Å

Experimental data
ReflectionsAll: 17656Test set: 900 (5.1%)
Resolution range39.43 Å2.24 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19700.19790.18270.1865
R-free0.24700.24080.21330.2218
σR-free 0.00800.00710.0074
Z(R-free) 1.452.772.16

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.700-0.714-0.747
2nd generation packing quality1-2.285-2.336-2.179
Ramachandran plot appearance1-1.768-1.362-1.390
Chi-1/Chi-2 rotamer normality1-2.016-1.015-1.055
Backbone conformation1-0.379-0.442-0.431
Bond length RMS Z-score20.4890.4540.465
Bond angle RMS Z-score20.6360.7160.719
Total number of bumps313107
Unsatisfied H-bond donors/acceptors3101511
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 residues5
Significantly deteriorated residues2
Changes of all residuesPlot

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