Optimised PDB entry 4k9i



Structure
SpacegroupP 21 21 21
Cell dimensionsa: 81.400 Åb: 90.895 Åc: 91.881 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution1.70 Å

Experimental data
ReflectionsAll: 74667Test set: 3766 (5.0%)
Resolution range45.45 Å1.70 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.18600.18120.19570.1968
R-free0.23800.22680.22260.2252
σR-free 0.00370.00360.0037
Z(R-free) -3.512.311.89

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.284-0.296-0.278
2nd generation packing quality1-1.760-1.763-1.606
Ramachandran plot appearance1-0.2300.1070.144
Chi-1/Chi-2 rotamer normality1-2.001-1.289-1.537
Backbone conformation1-0.220-0.270-0.237
Bond length RMS Z-score20.4580.5900.589
Bond angle RMS Z-score20.6510.7610.757
Total number of bumps3291417
Unsatisfied H-bond donors/acceptors3243125
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 residues8
Significantly deteriorated residues53
Changes of all residuesPlot

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