Optimised PDB entry 2ipk



Structure
SpacegroupH 3
Cell dimensionsa: 171.980 Åb: 171.980 Åc: 121.129 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.30 Å

Experimental data
ReflectionsAll: 67968Test set: 3438 (5.1%)
Resolution range32.50 Å2.19 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.20300.25430.15460.1554
R-free0.22400.26820.17900.1813
σR-free 0.00390.00330.0033
Z(R-free) 5.182.151.73

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.0590.0230.024
2nd generation packing quality1-1.489-1.355-1.189
Ramachandran plot appearance1-0.8410.0500.043
Chi-1/Chi-2 rotamer normality1-1.573-1.874-1.768
Backbone conformation10.4380.4170.393
Bond length RMS Z-score20.3150.6660.656
Bond angle RMS Z-score20.6450.8360.830
Total number of bumps3763945
Unsatisfied H-bond donors/acceptors3312421
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 residues331
Significantly deteriorated residues0
Changes of all residuesPlot

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