9QR3 | pdb_00009qr3

Methyl-coenzyme M reductase of an ANME-2c from a microbial enrichment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	2 ul protein at 24.6 g/l in 25 mM Tris/HCl pH 7.6, 10 % v/v glycerol, and 2 mM dithiothreitol was mixed with 2 ul crystallisation solution (30 % v/v 2-Methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM NaCl, and 8% polyethylene glycol 8000) on a Junior Clover plate (Jena Bioscience). The reservoir contained 90 ul of crystallisation solution.

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.867	α = 90
b = 157.456	β = 90.34
c = 215.422	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 EIGER X 16M		2022-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

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	1.34	127.16	96.2	0.168	0.183	0.073	0.991	6.6	6.3		1527343

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	1.34	1.5	66.6		1.671	1.829	0.737	0.56	1.6	6

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	1.34	98.93	1.34	1527210	76552	66.24	0.1142	0.1124	0.1139	0.1471	0.1465	15.77

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	14.295
f_angle_d	1.247
f_chiral_restr	0.088
f_plane_restr	0.016
f_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	76650
Nucleic Acid Atoms
Solvent Atoms	9812
Heterogen Atoms	986

Software

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