Optimised PDB entry 1jdi



Warnings!

Structure
SpacegroupP 4 21 2
Cell dimensionsa: 105.900 Åb: 105.900 Åc: 274.800 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution2.40 Å

Experimental data
ReflectionsAll: 58112Test set: 3283 (5.6%)
Resolution range14.98 Å2.40 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.20800.20570.16960.1666
R-free0.24100.24250.19750.1944
σR-free 0.00420.00340.0034
Z(R-free) 9.6210.5010.21

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-0.371-0.140-0.127
2nd generation packing quality1-0.4150.0030.300
Ramachandran plot appearance1-1.412-0.3280.043
Chi-1/Chi-2 rotamer normality1-4.027-2.196-0.660
Backbone conformation1-0.439-0.548-0.591
Bond length RMS Z-score20.3110.6280.507
Bond angle RMS Z-score20.6620.9150.775
Total number of bumps31952539
Unsatisfied H-bond donors/acceptors3525456
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 residues196
Significantly deteriorated residues1
Changes of all residuesPlot

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