11YC

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL12-2
Synchrotron site	SSRL
Beamline	BL12-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-11-08
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.73 1.85
Spacegroup name	P 41 21 2
Unit cell lengths	114.253, 114.253, 146.029
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	57.130 - 2.410
R-factor	0.195
Rwork	0.194
R-free	0.21950
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.543
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	57.130	2.496
High resolution limit [Å]	2.410	2.410
Rmerge	0.076	2.685
Rmeas	0.077	2.856
Rpim	0.016	0.936
Number of reflections	37632	3687
<I/σ(I)>	25.27	0.58
Completeness [%]	99.9	99.01
Redundancy	21.9	8.7
CC(1/2)	1.000	0.226

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	6	298	Ammonium Acetate, HEPES, Polyethylene glycol 3,350