PDB entry 3wd5



Structure
SpacegroupI 21 3
Cell dimensionsa: 161.849 Åb: 161.849 Åc: 161.849 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution3.10 Å

Experimental data
ReflectionsAll: 14578Test set: 733 (5.0%)
Resolution range46.72 Å2.98 Å

R-values etc.
From PDB headerCalculated from dataAfter conservative optimisationAfter full optimisation
R0.18700.20300.20300.1969
R-free0.27500.29240.29240.2778
σR-free 0.0108NA0.0103
R-free Z-score -4.56NA-4.08

WHAT_CHECK validation
Original PDB entryConservatively optimisedFully optimised
1st generation packing quality1-0.624-0.709-0.539
2nd generation packing quality1-0.739-0.879-0.635
Ramachandran plot appearance1-2.905-2.909-2.635
Chi-1/Chi-2 rotamer normality1-4.294-4.325-3.706
Backbone conformation1-0.224-0.225-0.281
Bond length RMS Z-score20.4340.4350.545
Bond angle RMS Z-score20.7010.7030.775
Total number of bumps3969694
Unsatisfied H-bond donors/acceptors3676752
Full WHAT_CHECK reportsLink LinkLink

1 Higher is better
2 Should be lower than 1.000
3 Fewer is better

Electron density map validation
Real-space correlation coefficientReal-space R-factor
Significantly improved residues139
Significantly deteriorated residues00
Changes of all residuesPlot Plot

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