9QQT

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 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	2024-02-15
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97930
Spacegroup name	P 1 21 1
Unit cell lengths	81.621, 189.823, 83.930
Unit cell angles	90.00, 114.36, 90.00

Refinement procedure

Resolution	41.710 - 0.980
R-factor	0.1293
Rwork	0.128
R-free	0.14810
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.011
RMSD bond angle	1.382
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]	94.911	1.035
High resolution limit [Å]	0.977	0.977
Rmerge	0.079	0.800
Rmeas	0.085	0.863
Rpim	0.030	0.320
Number of reflections	996827	49841
<I/σ(I)>	13	1.9
Completeness [%]	83.9	62.6
Redundancy	7.6	7
CC(1/2)	0.998	0.754

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.9	291.15	Crystals were produced on a Junior Clover plate using a crystallization solution containing 20 % w/v polyethylene glycol 3,350 and 200 mM sodium thiocyanate pH 6.9. The reservoir contained 100 ul crystallization solution and drops of 2 ul solution were mixed with 3 ul protein at a concentration of 40 mg/ml in 25 mM Tris/HCl pH 8.0, 10% v/v glycerol, 100 mM NaCl and 2 mM dithiothreitol. Crystals were soaked in the crystallization solution containing 20 % v/v ethylene glycol before freezing in liquid nitrogen.