Optimised PDB entry 2toh



Structure
SpacegroupF 2 2 2
Cell dimensionsa: 189.464 Åb: 148.595 Åc: 56.986 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.30 Å

Experimental data
ReflectionsAll: 17447Test set: 1200 (6.9%)
Resolution range39.94 Å2.29 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.20700.21220.18670.1879
R-free0.27600.28490.24910.2501
σR-free 0.00820.00720.0072
Z(R-free) -0.120.100.18

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.894-0.564-0.552
2nd generation packing quality1-2.031-1.576-1.388
Ramachandran plot appearance1-3.054-1.027-0.993
Chi-1/Chi-2 rotamer normality1-5.085-3.461-2.355
Backbone conformation1-1.243-0.745-0.916
Bond length RMS Z-score20.8290.5310.529
Bond angle RMS Z-score21.0300.7830.777
Total number of bumps3551816
Unsatisfied H-bond donors/acceptors3302628
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 residues51
Significantly deteriorated residues2
Changes of all residuesPlot

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