9RWD

High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-05-29
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0597
Spacegroup name	P 1 21 1
Unit cell lengths	59.184, 125.571, 135.137
Unit cell angles	90.00, 93.67, 90.00

Refinement procedure

Resolution	59.060 - 1.300
R-factor	0.1452
Rwork	0.145
R-free	0.17820
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.831
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	80.000	1.380
High resolution limit [Å]	1.300	1.300
Rmerge	0.057	0.814
Rmeas	0.062	0.902
Number of reflections	469350	68295
<I/σ(I)>	17.9	1.93
Completeness [%]	97.7	87.9
Redundancy	6.67	5.29
CC(1/2)	0.999	0.611

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	70 mM Tris pH 8.5, 4.375% PEG 2000, 4.375% PEG 3350, 4.375% PEG 4000, 4.375% PEG methyl ether 5000, 30% ethylene glycol