9QR1 | pdb_00009qr1

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished model (deposition D_1292146335)

Crystallization

Crystalization Experiments
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.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.575	α = 90
b = 189.299	β = 114.27
c = 84.109	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2023-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.97980	ESRF	BM07

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	0.976	76.674	96.5	0.119	0.128	0.045	0.996	9.4	7.8		1130261

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.976	1.04	70.9		1.168	1.26	0.468	0.667	1.7	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	0.98	41.78	1.34	1130120	57217	84.39	0.1033	0.1025	0.1251	0.1176	0.1331	10.72

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.075
f_angle_d	1.341
f_chiral_restr	0.099
f_plane_restr	0.016
f_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18876
Nucleic Acid Atoms
Solvent Atoms	3419
Heterogen Atoms	287

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing