Optimised PDB entry 1d3c



Warnings!

Structure
SpacegroupP 21 21 21
Cell dimensionsa: 117.791 Åb: 109.532 Åc: 65.223 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution1.78 Å

Experimental data
ReflectionsAll: 77755Test set: 0 (0.0%)
Resolution range51.87 Å1.78 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.22000.20840.18600.1846
R-free0.25800.20760.22150.2206
σR-free 0.00330.00350.0035
Z(R-free) 11.85-0.37-0.57

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.134-0.061-0.062
2nd generation packing quality1-1.089-0.903-0.880
Ramachandran plot appearance1-1.753-0.654-0.678
Chi-1/Chi-2 rotamer normality1-3.081-1.296-1.196
Backbone conformation1-1.000-0.920-0.929
Bond length RMS Z-score20.3350.4890.485
Bond angle RMS Z-score20.4980.7020.687
Total number of bumps31783227
Unsatisfied H-bond donors/acceptors3383131
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 residues57
Significantly deteriorated residues0
Changes of all residuesPlot

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