9QR1

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens sp. BLZ2 from a bioreactor enrichment culture

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE BM07
Synchrotron site	ESRF
Beamline	BM07
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-03-30
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97980
Spacegroup name	P 1 21 1
Unit cell lengths	81.575, 189.299, 84.109
Unit cell angles	90.00, 114.27, 90.00

Refinement procedure

Resolution	41.780 - 0.980
R-factor	0.1033
Rwork	0.102
R-free	0.11760
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.341
Data reduction software	autoPROC
Data scaling software	STARANISO
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	76.674	1.040
High resolution limit [Å]	0.976	0.976
Rmerge	0.119	1.168
Rmeas	0.128	1.260
Rpim	0.045	0.468
Number of reflections	1130261	56513
<I/σ(I)>	9.4	1.7
Completeness [%]	96.5	70.9
Redundancy	7.8	7.1
CC(1/2)	0.996	0.667

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8	291.15	Crystallisation was carried out on a junior Clover plate using a solution containing 20% w/v polyethylene glycol 3,350, 50 mM Tris pH 8.0, and 200 mM potassium nitrate. The reservoir contained 100 ul of crystallisation solution. 5 ul protein at 2.19 mg/ml in 25 mM Tris/HCl pH 8.0, 100 mM NaCl, 10% v/v glycerol and 2 mM dithiothreitol were mixed with 2 ul of the crystallisation solution. Crystals were soaked in a crystallisation solution supplemented with 20% ethylene glycol before freezing in liquid nitrogen.