9M5W

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K 1.58 angstrom

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]	343
Detector technology	PIXEL
Collection date	2024-11-24
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	H 3 2
Unit cell lengths	78.940, 78.940, 233.481
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	44.390 - 1.580
Rwork	0.141
R-free	0.16280
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1wta
RMSD bond length	0.012
RMSD bond angle	1.981
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0430 (refmacat 0.4.82))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	44.390	44.390	1.610
High resolution limit [Å]	1.580	8.650	1.580
Rmerge	0.058	0.018	1.047
Rmeas	0.065	0.020	1.166
Rpim	0.028	0.009	0.509
Number of reflections	38817	279	1901
<I/σ(I)>	25.7	93.5	2.4
Completeness [%]	99.9	98.5	100
Redundancy	10	8.2	10.2
CC(1/2)	1.000	1.000	0.669

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	COUNTER-DIFFUSION	5.4	293.2	The mixture of protein solution and agarose was 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 pH 5.4, 5mM MTA