9NIN

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-86

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	2024-04-08
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.979460
Spacegroup name	P 41 21 2
Unit cell lengths	113.159, 113.159, 145.684
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	61.250 - 2.010
R-factor	0.185
Rwork	0.183
R-free	0.21170
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.867
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]	61.250	2.082
High resolution limit [Å]	2.010	2.010
Rmerge	0.196	6.429
Rmeas	0.200	6.584
Rpim	0.041	1.366
Number of reflections	60721	4720
<I/σ(I)>	12.49	0.74
Completeness [%]	94.7
Redundancy	24	22.6
CC(1/2)	0.993	0.029

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	6	298	0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10,000