Optimised PDB entry 1dpx

Warnings!

R-free set could not be extracted from structure factor file
A new R-free set (7.2% of all reflections) was created for this optimisation

Structure
Spacegroup	P 43 21 2
Cell dimensions	a: 77.050 Å	b: 77.050 Å	c: 37.210 Å
	α: 90.00°	β: 90.00°	γ: 90.00°
Resolution	1.65 Å

Experimental data
Reflections	All: 13961	Test set: 0 (0.0%)
Resolution range	38.53 Å	1.65 Å

R-values etc.
	From PDB header	Calculated from data	After re-refinement	After re-refinement and rebuilding
R	0.1870	0.1792	0.1673	0.1666
R-free	0.2460	0.1827	0.1984	0.2036
σR-free		0.0057	0.0062	0.0064
Z(R-free)		5.54	0.27	-0.69

WHAT_CHECK validation
	Original PDB entry	Re-refined (only)	Re-refined and rebuilt
1st generation packing quality¹	-1.427	-1.427	-1.408
2nd generation packing quality¹	-0.245	-0.300	-0.206
Ramachandran plot appearance¹	-0.902	-1.045	-1.083
Chi-1/Chi-2 rotamer normality¹	-0.604	-0.911	-0.513
Backbone conformation¹	-1.873	-1.929	-1.987
Bond length RMS Z-score²	0.480	0.702	0.683
Bond angle RMS Z-score²	1.180	0.835	0.831
Total number of bumps³	5	9	5
Unsatisfied H-bond donors/acceptors³	5	4	3
	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	7
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