5YLU

Crystal structure of the gastric proton pump complexed with vonoprazan

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL41XU
Synchrotron site	SPring-8
Beamline	BL41XU
Temperature [K]	80
Detector technology	PIXEL
Collection date	2017-05-30
Detector	DECTRIS PILATUS3 S 6M
Wavelength(s)	1.0
Spacegroup name	P 31 2 1
Unit cell lengths	104.820, 104.820, 367.080
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	48.177 - 2.800
R-factor	0.239318208654
Rwork	0.237
R-free	0.28836
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5y0b
RMSD bond length	0.011
RMSD bond angle	1.313
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	phenix.refine (1.11.1_2575)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.180	2.900
High resolution limit [Å]	2.800	2.800
Rmerge	0.120	1.689
Rpim	0.057	0.787
Number of reflections	58652	31309
<I/σ(I)>	11.04	1.54
Completeness [%]	87.5	38.17
Redundancy	5.2	5.5

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	10% glycerol, 20% PEG2000MME, 0.4M CH3COONa, 3% methylpentanediol, 5mM beta-mercaptoethanol