Optimised PDB entry 1pyw



Structure
SpacegroupH 3
Cell dimensionsa: 172.507 Åb: 172.507 Åc: 121.652 Å
α: 90.00°β: 90.00°γ: 120.00°
Resolution2.10 Å

Experimental data
ReflectionsAll: 78492Test set: 7813 (10.0%)
Resolution range21.31 Å2.08 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.20900.20460.18060.1761
R-free0.23500.22600.20740.2022
σR-free 0.00260.00230.0023
Z(R-free) 5.311.871.83

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.102-0.056-0.082
2nd generation packing quality1-1.473-1.535-1.208
Ramachandran plot appearance1-0.9550.2310.364
Chi-1/Chi-2 rotamer normality1-2.302-1.795-1.584
Backbone conformation1-0.142-0.189-0.083
Bond length RMS Z-score20.2870.6150.584
Bond angle RMS Z-score20.6250.8140.797
Total number of bumps3693723
Unsatisfied H-bond donors/acceptors3323032
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 residues235
Significantly deteriorated residues0
Changes of all residuesPlot

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