9VS8

Intermediate state structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix at high temperature (363K) after 10 minutes reaction with substrate

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-17A
Synchrotron site	Photon Factory
Beamline	BL-17A
Temperature [K]	363
Detector technology	PIXEL
Collection date	2025-07-02
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	H 3 2
Unit cell lengths	79.042, 79.042, 233.625
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	44.430 - 2.080
Rwork	0.144
R-free	0.17410
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1wta
RMSD bond length	0.008
RMSD bond angle	1.746
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0430 (refmacat 0.4.105))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	44.430	44.430	2.140
High resolution limit [Å]	2.080	9.070	2.080
Rmerge	0.194	0.034	1.123
Rmeas	0.215	0.038	1.242
Rpim	0.092	0.017	0.526
Number of reflections	17322	243	1335
<I/σ(I)>	13.2	44.2	2.6
Completeness [%]	100.0	98.3	100
Redundancy	10.2	7.7	10.7
CC(1/2)	0.997	0.999	0.674

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	COUNTER-DIFFUSION	5.4	293.2	The mixture of protein solution and agarose, methylcellulose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows. 15%(v/v)PEG#200, 0.1M phosphate citrate pH5.4, 5mM MTA