PDB entry 1jdi


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 conservative optimisationAfter full optimisation
σR-free 0.00300.00250.0024
R-free Z-score 13.0015.4813.25

WHAT_CHECK validation
Original PDB entryConservatively optimisedFully optimised
1st generation packing quality1-0.372-0.154-0.072
2nd generation packing quality1-0.912-0.729-0.220
Ramachandran plot appearance1-0.5360.3600.507
Chi-1/Chi-2 rotamer normality1-2.729-1.279-0.403
Backbone conformation10.4670.4450.491
Bond length RMS Z-score20.3110.5390.506
Bond angle RMS Z-score20.6620.8110.751
Total number of bumps32378046
Unsatisfied H-bond donors/acceptors3423046
Full WHAT_CHECK reportsLink LinkLink

1 Higher is better
2 Should be lower than 1.000
3 Fewer is better

Electron density map validation
Real-space correlation coefficientReal-space R-factor
Significantly improved residues216121
Significantly deteriorated residues01
Changes of all residuesPlot Plot