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
R0.19700.19840.17870.1838
R-free0.24700.24060.21270.2201
σR-free 0.00800.00710.0073
Z(R-free) 1.552.141.96

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.3170.3340.318
2nd generation packing quality1-1.790-1.927-1.772
Ramachandran plot appearance1-1.353-1.333-1.376
Chi-1/Chi-2 rotamer normality1-2.113-1.585-1.753
Backbone conformation12.8882.8202.766
Bond length RMS Z-score20.4890.5790.594
Bond angle RMS Z-score20.6360.7950.809
Total number of bumps3521915
Unsatisfied H-bond donors/acceptors3111213
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 residues7
Significantly deteriorated residues0
Changes of all residuesPlot

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