9JFN

Arginine decarboxylase in Aspergillus oryzae complexed with agmatine

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)	1.000
Spacegroup name	C 2 2 21
Unit cell lengths	133.749, 197.286, 196.412
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	43.490 - 2.150
R-factor	0.1777
Rwork	0.176
R-free	0.21350
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold
RMSD bond length	0.006
RMSD bond angle	0.795
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	2.280
High resolution limit [Å]	2.150	2.150
Rmerge	0.009	0.968
Rmeas	0.010	1.022
Number of reflections	140013	22183
<I/σ(I)>	17.86	2.47
Completeness [%]	99.7	98.6
Redundancy	9.19	9.53
CC(1/2)	0.999	0.884

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING 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 10 mM L-agmatine for 10 min. followed by brief soaking to the same solution containing 30% ethylene glycol before flash-cooling.