6M5W

Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL26B2
Synchrotron site	SPring-8
Beamline	BL26B2
Temperature [K]	100
Detector technology	CCD
Collection date	2019-04-19
Detector	RAYONIX MX225-HS
Wavelength(s)	1.0
Spacegroup name	P 62 2 2
Unit cell lengths	152.749, 152.749, 235.933
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	46.680 - 3.100
R-factor	0.1956
Rwork	0.194
R-free	0.23290
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1bj4
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHENIX
Refinement software	PHENIX (1.11)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	46.680	46.680	3.290
High resolution limit [Å]	3.100	9.160	3.100
Rmerge	0.526	0.056	4.157
Rmeas	0.550	0.059	4.345
Total number of observations	659305
Number of reflections	55751	2159	8964
<I/σ(I)>	7.31	42.13	0.91
Completeness [%]	99.9	99.2	99.9
Redundancy	11.826	11.664	11.737
CC(1/2)	0.992	0.999	0.586

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M potassium chloride, 0.05 M HEPES pH 7.5, and 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH)