7B1S | pdb_00007b1s

Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum at 0.994-A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	Crystals were obtained by initial screening at 20 degree celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor, crystallization drop contained a mixture of 0.6 ul protein at 16.22 mg.ml-1 and 0.6 ul precipitant. The crystal was obtained by initial screening using the JBScreen Pentaerythritol screen from Jena Bioscience in a Coy tent under an N2/H2 atmosphere (95:5 %). The crystallization reservoir contained 45 % (w/v) Pentaerythritol Propoxylate (5/4 PO/OH), 100 mM Tris pH 8.5 and 400 mM potassium chloride.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.736	α = 90
b = 146.927	β = 106.98
c = 113.128	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 2M-F		2019-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00003	SLS	X06DA

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	0.992	108.19	89.1	0.116	0.125	0.047	0.997	9.7	7		1061996

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	0.992	1.07	58.1		1.167	1.262	0.476	0.563	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	5A8W	0.992	39.76	1.35	1045444	52845	73.39	0.1127	0.1119	0.13	0.1275	0.14	10.6019

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20525
Nucleic Acid Atoms
Solvent Atoms	3086
Heterogen Atoms	261

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.