8BYH

Crystal structure of TrmD domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P14 (MX2)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-10-27
Detector	DECTRIS EIGER2 X CdTe 16M
Wavelength(s)	0.465220
Spacegroup name	P 43 21 2
Unit cell lengths	85.390, 85.390, 210.710
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.830 - 2.190
R-factor	0.1687
Rwork	0.167
R-free	0.20880
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	8b1n
RMSD bond length	0.007
RMSD bond angle	0.857
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.17.1_3660)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	45.790	2.320
High resolution limit [Å]	2.190	2.190
Rmeas	0.133	1.018
Number of reflections	40840	6191
<I/σ(I)>	11.93	1.8
Completeness [%]	99.1	95.1
Redundancy	8.75	5.67
CC(1/2)	0.998	0.720

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein sample: 4 mg/mL TrmD in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, 10 mM SAM, 20 mM MgCl2. Reservoir solution: 0.2 M sodium thiocyanate, 20% w/v PEG 3350 (JCSG+ screen 1-14).