PDB entry 1dpx

Warnings!

A new R-free set (0.0716 fraction 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 conservative optimisation	After full optimisation
R	0.1870	0.1794	0.1704	0.1716
R-free	0.2460	0.2074	0.2132	0.2143
σR-free		0.0047	0.0048	0.0048
R-free Z-score		1.51	-1.98	-1.90

WHAT_CHECK validation
	Original PDB entry	Conservatively optimised	Fully optimised
1st generation packing quality¹	-1.427	-1.399	-1.379
2nd generation packing quality¹	0.313	0.287	0.445
Ramachandran plot appearance¹	-0.251	-0.565	-0.376
Chi-1/Chi-2 rotamer normality¹	-0.309	-0.237	0.048
Backbone conformation¹	-0.586	-0.927	-1.025
Bond length RMS Z-score²	0.480	0.609	0.599
Bond angle RMS Z-score²	1.180	0.772	0.751
Total number of bumps³	23	17	15
Unsatisfied H-bond donors/acceptors³	1	7	7
Full WHAT_CHECK reports	Link	Link	Link

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

Electron density map validation
	Real-space correlation coefficient	Real-space R-factor
Significantly improved residues	4	13
Significantly deteriorated residues	0	0
Changes of all residues	Plot	Plot

Download

Conservatively optimised structure (PDB | MTZ)
Fully optimised structure (PDB | MTZ)
YASARA scenes (for visualisation of the results)
All files (compressed)

Links