Optimised PDB entry 4m9n

Structure
Spacegroup	P 1 21 1
Cell dimensions	a: 54.523 Å	b: 79.215 Å	c: 54.685 Å
	α: 90.00°	β: 106.24°	γ: 90.00°
Resolution	2.27 Å

Experimental data
Reflections	All: 19941	Test set: 1987 (10.0%)
Resolution range	13.92 Å	2.28 Å

R-values etc.
	From PDB header	Calculated from data	After re-refinement	After re-refinement and rebuilding
R	0.1920	0.2056	0.1975	0.1956
R-free	0.2270	0.2406	0.2257	0.2336
σR-free		0.0054	0.0051	0.0052
Z(R-free)		6.43	7.59	5.44

WHAT_CHECK validation
	Original PDB entry	Re-refined (only)	Re-refined and rebuilt
1st generation packing quality¹	-0.123	-0.186	-0.129
2nd generation packing quality¹	-0.764	-0.694	0.147
Ramachandran plot appearance¹	-0.242	0.111	0.016
Chi-1/Chi-2 rotamer normality¹	-0.046	0.052	-0.369
Backbone conformation¹	-0.489	-0.550	-0.605
Bond length RMS Z-score²	0.313	0.362	0.362
Bond angle RMS Z-score²	0.560	0.632	0.645
Total number of bumps³	34	18	18
Unsatisfied H-bond donors/acceptors³	7	6	6
	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	3
Significantly deteriorated residues	3
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