Optimised PDB entry 1jyu



Warnings!

Structure
SpacegroupI 4 2 2
Cell dimensionsa: 81.329 Åb: 81.329 Åc: 80.697 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.75 Å

Experimental data
ReflectionsAll: 3697Test set: 0 (0.0%)
Resolution range23.42 Å2.75 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.23100.22160.17400.1664
R-free0.28700.23160.21480.2258
σR-free 0.01240.01150.0121
Z(R-free) 2.77-0.52-2.16

Cross validation results
RR-freeDifferenceTest set size
Average0.16790.21760.0496370
σ-value0.00180.00760.008739

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-2.673-1.918-1.852
2nd generation packing quality1-0.7380.5660.976
Ramachandran plot appearance1-4.020-0.231-0.942
Chi-1/Chi-2 rotamer normality1-6.865-2.671-1.254
Backbone conformation1-0.266-0.187-0.151
Bond length RMS Z-score20.6160.3920.370
Bond angle RMS Z-score20.9740.7120.646
Total number of bumps33132
Unsatisfied H-bond donors/acceptors3535
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 residues28
Significantly deteriorated residues0
Changes of all residuesPlot

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