Optimised PDB entry 1pya



Warnings!

Structure
SpacegroupI 41 2 2
Cell dimensionsa: 221.700 Åb: 221.700 Åc: 107.100 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.50 Å

Experimental data
ReflectionsAll: 45944Test set: 0 (0.0%)
Resolution range49.57 Å2.50 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.15000.15370.12300.1212
R-freeNA0.14710.15010.1494
σR-free 0.00310.00320.0032
Z(R-free) 18.554.253.72

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.494-0.456-0.397
2nd generation packing quality1-1.584-1.437-1.080
Ramachandran plot appearance1-1.100-0.198-0.136
Chi-1/Chi-2 rotamer normality1-4.529-3.766-2.182
Backbone conformation1-0.105-0.129-0.158
Bond length RMS Z-score20.7540.8990.868
Bond angle RMS Z-score21.5271.1231.026
Total number of bumps3161817
Unsatisfied H-bond donors/acceptors3556659
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 residues336
Significantly deteriorated residues0
Changes of all residuesPlot

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