Optimised PDB entry 1t5x

Structure
Spacegroup	H 3
Cell dimensions	a: 173.208 Å	b: 173.208 Å	c: 121.543 Å
	α: 90.00°	β: 90.00°	γ: 120.00°
Resolution	2.50 Å

Experimental data
Reflections	All: 53191	Test set: 5334 (10.0%)
Resolution range	29.78 Å	2.39 Å

R-values etc.
	From PDB header	Calculated from data	After re-refinement	After re-refinement and rebuilding
R	0.2080	0.2566	0.1898	0.1905
R-free	0.2410	0.2775	0.2167	0.2156
σR-free		0.0038	0.0030	0.0030
Z(R-free)		9.45	5.03	5.67

WHAT_CHECK validation
	Original PDB entry	Re-refined (only)	Re-refined and rebuilt
1st generation packing quality¹	-0.206	-0.200	-0.142
2nd generation packing quality¹	-1.489	-1.364	-1.094
Ramachandran plot appearance¹	-1.669	-0.400	-0.070
Chi-1/Chi-2 rotamer normality¹	-2.650	-2.473	-1.813
Backbone conformation¹	0.346	0.271	0.373
Bond length RMS Z-score²	0.299	0.529	0.431
Bond angle RMS Z-score²	0.619	0.756	0.672
Total number of bumps³	64	24	18
Unsatisfied H-bond donors/acceptors³	34	24	29
	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	120
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