9LVZ

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 323K

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]	323
Detector technology	PIXEL
Collection date	2024-10-27
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	H 3 2
Unit cell lengths	79.065, 79.065, 233.167
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	44.390 - 1.590
Rwork	0.145
R-free	0.17050
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1wta
RMSD bond length	0.012
RMSD bond angle	1.927
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	1.620
High resolution limit [Å]	1.590	8.710	1.590
Rmerge	0.116	0.036	1.076
Rmeas	0.130	0.040	1.198
Rpim	0.057	0.019	0.521
Number of reflections	38232	275	1899
<I/σ(I)>	17.2	44.2	2.7
Completeness [%]	100.0	98.9	100
Redundancy	9.8	7.1	10.1
CC(1/2)	0.999	0.997	0.667

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