Optimised PDB entry 2vck



Structure
SpacegroupP 1
Cell dimensionsa: 53.560 Åb: 67.570 Åc: 81.280 Å
α: 92.26°β: 109.07°γ: 106.58°
Resolution1.80 Å

Experimental data
ReflectionsAll: 91990Test set: 4819 (5.2%)
Resolution range49.19 Å1.80 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.18400.18160.16970.1653
R-free0.22500.21750.19390.1919
σR-free 0.00310.00280.0028
Z(R-free) -0.392.931.79

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.393-0.358-0.354
2nd generation packing quality1-1.551-1.555-1.583
Ramachandran plot appearance1-1.685-1.114-1.067
Chi-1/Chi-2 rotamer normality1-2.126-1.393-1.057
Backbone conformation1-0.777-0.713-0.669
Bond length RMS Z-score20.6080.6780.813
Bond angle RMS Z-score20.7120.8550.921
Total number of bumps3473238
Unsatisfied H-bond donors/acceptors3354041
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 residues51
Significantly deteriorated residues0
Changes of all residuesPlot

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