Optimised PDB entry 1jo8

Structure
Spacegroup	P 21 21 21
Cell dimensions	a: 24.080 Å	b: 38.155 Å	c: 59.090 Å
	α: 90.00°	β: 90.00°	γ: 90.00°
Resolution	1.30 Å

Experimental data
Reflections	All: 13707	Test set: 680 (5.0%)
Resolution range	17.50 Å	1.30 Å

R-values etc.
	From PDB header	Calculated from data	After re-refinement	After re-refinement and rebuilding
R	0.1440	0.1455	0.1160	0.1170
R-free	0.1780	0.1807	0.1513	0.1509
σR-free		0.0069	0.0058	0.0058
Z(R-free)		3.64	2.21	2.52

WHAT_CHECK validation
	Original PDB entry	Re-refined (only)	Re-refined and rebuilt
1st generation packing quality¹	-0.107	-0.176	-0.179
2nd generation packing quality¹	2.001	1.993	1.997
Ramachandran plot appearance¹	-0.418	-0.222	-0.202
Chi-1/Chi-2 rotamer normality¹	1.088	1.303	1.466
Backbone conformation¹	1.100	1.109	1.106
Bond length RMS Z-score²	0.486	0.766	0.762
Bond angle RMS Z-score²	0.795	0.893	0.886
Total number of bumps³	0	0	0
Unsatisfied H-bond donors/acceptors³	2	2	2
	Link	Link	Link

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

Density map fit (real-space correlation coefficient)
Significantly improved residues	61
Significantly deteriorated residues	0
Changes of all residues	Plot

Download

Re-refined and rebuilt structure (PDB | MTZ)
Re-refined (only) structure (PDB | MTZ)
YASARA scenes (for visualisation of the results)
All files (compressed)

Links