8CNR

Hybrid Cluster Protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus as isolated in a reduced state at 1.45-A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293.15	Crystallisation was performed anaerobically at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a N2/H2 (97:3%) atmosphere. The reservoir chamber was filled with 90 ul of crystallisation condition and the drop was formed by spotting 0.55 ul protein with 0.55 ul of 20% (w/v) PEG 3,350 and 200 mM Magnesium formate. The protein was crystallized at 9.9 mg/ml in 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol and 10% (v/v) glycerol. Densities in the electron density map suggest a contamination from another crystallisation condition spatially close and containing 30% (v/v) 2-Methyl-2,4-pentanediol, 20 mM Calcium chloride and 100 mM Sodium acetate, pH 4.6. Crystals were cryo-protected by soaking in 20% (w/v) PEG 3,350 and 200mM Magnesium formate supplemented with 20% v/v glycerol for a few seconds.

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.557	α = 90
b = 102.454	β = 90
c = 58.896	γ = 90

Symmetry
Space Group	P 21 21 2

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		2020-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.23984	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	1.45	51.061	98.8	0.119	0.132	0.056	0.996	9.5	5.3		103697

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	1.451	1.476	92.4		1.193	1.361	0.642	0.51	1.4

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.45	51.06	1.34	103571	5332	98.66	0.1341	0.1331	0.1524	19.51

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	13.639
f_angle_d	1.288
f_chiral_restr	0.093
f_plane_restr	0.011
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4236
Nucleic Acid Atoms
Solvent Atoms	649
Heterogen Atoms	68

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
SHELXDE	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 R01GM133198.