PDB entry 3pgd



Structure
SpacegroupP 43 21 2
Cell dimensionsa: 94.449 Åb: 94.449 Åc: 275.535 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.72 Å

Experimental data
ReflectionsAll: 34493Test set: 1725 (5.0%)
Resolution range33.52 Å2.72 Å

R-values etc.
From PDB headerCalculated from dataAfter conservative optimisationAfter full optimisation
R0.19600.20250.19270.1924
R-free0.24200.24610.22970.2306
σR-free 0.00590.00550.0056
Z(R-free) -0.530.270.05

WHAT_CHECK validation
Original PDB entryConservatively optimisedFully optimised
1st generation packing quality1-0.0140.1690.121
2nd generation packing quality1-1.249-0.991-0.838
Ramachandran plot appearance1-1.170-0.408-0.458
Chi-1/Chi-2 rotamer normality1-3.009-1.804-1.572
Backbone conformation11.0221.0610.918
Bond length RMS Z-score20.3790.3630.357
Bond angle RMS Z-score20.6000.6050.604
Total number of bumps31024451
Unsatisfied H-bond donors/acceptors3373732
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 residues27
Significantly deteriorated residues3
Changes of all residuesPlot

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