Optimised PDB entry 4ivd



Structure
SpacegroupP 1 21 1
Cell dimensionsa: 42.795 Åb: 173.608 Åc: 44.629 Å
α: 90.00°β: 94.53°γ: 90.00°
Resolution1.93 Å

Experimental data
ReflectionsAll: 48312Test set: 2259 (4.7%)
Resolution range41.43 Å1.93 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.20200.20210.19250.1863
R-free0.24700.24820.22780.2209
σR-free 0.00520.00480.0046
Z(R-free) -0.231.541.48

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.844-0.727-0.705
2nd generation packing quality1-0.369-0.273-0.199
Ramachandran plot appearance1-1.426-0.676-0.601
Chi-1/Chi-2 rotamer normality1-1.667-1.391-1.051
Backbone conformation1-0.559-0.473-0.402
Bond length RMS Z-score20.4520.5440.518
Bond angle RMS Z-score20.5860.7330.712
Total number of bumps3342023
Unsatisfied H-bond donors/acceptors3221521
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 residues7
Changes of all residuesPlot

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