9ZF4

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL12-1
Synchrotron site	SSRL
Beamline	BL12-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-11-12
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.979460
Spacegroup name	P 41 21 2
Unit cell lengths	113.074, 113.074, 145.461
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	61.170 - 2.090
R-factor	0.1934
Rwork	0.192
R-free	0.22370
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.882
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]	61.170	2.165
High resolution limit [Å]	2.090	2.090
Rmerge	0.019	0.617
Rmeas	0.026	0.872
Rpim	0.019	0.617
Number of reflections	56386	5552
<I/σ(I)>	24.81	1.11
Completeness [%]	100.0	99.89
Redundancy	2	2
CC(1/2)	1.000	0.466

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	297	0.2 M Sodium Chloride, 25% w/v Polyethylene glycol 3,350