Optimised PDB entry 3vt5



Structure
SpacegroupC 1 2 1
Cell dimensionsa: 153.174 Åb: 42.565 Åc: 42.184 Å
α: 90.00°β: 96.10°γ: 90.00°
Resolution2.11 Å

Experimental data
ReflectionsAll: 14420Test set: 1453 (10.1%)
Resolution range40.99 Å2.11 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.22400.21410.18660.1847
R-free0.26600.25640.23420.2338
σR-free 0.00670.00610.0061
Z(R-free) 3.361.441.11

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality10.4800.5290.529
2nd generation packing quality10.0220.1440.247
Ramachandran plot appearance1-1.080-0.079-0.040
Chi-1/Chi-2 rotamer normality1-1.440-2.020-2.161
Backbone conformation1-0.923-0.907-0.957
Bond length RMS Z-score20.2350.5130.529
Bond angle RMS Z-score20.4720.7180.722
Total number of bumps3191110
Unsatisfied H-bond donors/acceptors39129
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 residues88
Significantly deteriorated residues0
Changes of all residuesPlot

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