9JF5

Arginine decarboxylase in Aspergillus oryzae complexed with arginine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL26B1
Synchrotron site	SPring-8
Beamline	BL26B1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-05-12
Detector	DECTRIS EIGER R 4M
Wavelength(s)	1.00
Spacegroup name	C 2 2 21
Unit cell lengths	134.020, 195.575, 196.124
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.440 - 1.900
R-factor	0.1617
Rwork	0.160
R-free	0.18890
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold
RMSD bond length	0.006
RMSD bond angle	0.802
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHENIX
Refinement software	PHENIX (1.21.1_5286)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.020
High resolution limit [Å]	1.900	1.900
Rmerge	0.082	0.847
Rmeas	0.088	0.911
Number of reflections	200882	32042
<I/σ(I)>	18.02	2.26
Completeness [%]	99.8	99.2
Redundancy	7.66	7.26
CC(1/2)	0.999	0.808

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M sodium acetate buffer (pH 7.0), 12% w/v PEG 3350. The crystal was soaked in the reservoir solution with 1 mM L-arginine for 10 min before flash-cooling.