9JD2

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K

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]	353
Detector technology	PIXEL
Collection date	2024-06-02
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0
Spacegroup name	H 3 2
Unit cell lengths	79.048, 79.048, 233.480
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	38.944 - 1.620
Rwork	0.123
R-free	0.16760
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1wta
RMSD bond length	0.009
RMSD bond angle	1.688
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0430 (refmacat 0.4.77))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	39.520	39.520	1.650
High resolution limit [Å]	1.620	8.870	1.620
Rmerge	0.141	0.030	2.545
Rmeas	0.157	0.033	2.838
Rpim	0.069	0.015	1.246
Number of reflections	36182	259	1763
<I/σ(I)>	9.8	25.8	1.1
Completeness [%]	100.0	97.4	100
Redundancy	9.9	8	10
CC(1/2)	0.999	0.999	0.344

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	COUNTER-DIFFUSION	5.4	293.2	The mixture of protein solution and agarose 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#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA