9SDV

tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus in complex with SAM-competitive compound

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-11-15
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.9763
Spacegroup name	P 43 3 2
Unit cell lengths	126.695, 126.695, 126.695
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.230 - 2.500
R-factor	0.2252
Rwork	0.222
R-free	0.28040
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.190
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	56.660	2.600
High resolution limit [Å]	2.500	2.500
Rmerge	0.062	0.466
Rmeas	0.063	0.469
Rpim		0.054
Number of reflections	12606	1378
<I/σ(I)>	66.6
Completeness [%]	100.0	100
Redundancy	78.9
CC(1/2)	1.000	0.993

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.4	294	8mg/mL protein in 1.4M Na Malonate pH 7.4, 0.1M Bis-Tris Propane