Optimised PDB entry 1neg



Warnings!

Structure
SpacegroupP 43 21 2
Cell dimensionsa: 41.865 Åb: 41.865 Åc: 92.865 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.30 Å

Experimental data
ReflectionsAll: 3876Test set: 0 (0.0%)
Resolution range31.09 Å2.29 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.20000.20900.19830.1960
R-free0.24900.20870.24050.2394
σR-free 0.01040.01200.0119
Z(R-free) 6.541.831.68

Cross validation results
RR-freeDifferenceTest set size
Average0.19590.23990.0441388
σ-value0.00120.00910.009830

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-1.544-1.476-1.495
2nd generation packing quality11.3141.2581.145
Ramachandran plot appearance1-1.205-0.945-1.118
Chi-1/Chi-2 rotamer normality1-3.163-2.150-1.955
Backbone conformation11.2411.2211.189
Bond length RMS Z-score20.4190.4860.474
Bond angle RMS Z-score20.6920.7070.701
Total number of bumps3822
Unsatisfied H-bond donors/acceptors3532
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 residues1
Significantly deteriorated residues0
Changes of all residuesPlot

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