9R52 | pdb_00009r52

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9R51

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3%) atmosphere at 20 degree Celsius using the sitting/drop method in CombiClover crystallisation plates. The enzyme was used at a concentration of 6.1 mg/ml in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, 2 mM dithiothreitol and 2 mM flavin adenine dinucleotide (FAD). 2 ul of the protein sample was mixed with 2 ul of the following crystallisation solution made of 45 % (w/v) Pentaerythritol propoxylate (17/8 PO/OH) and 100 mM Tris pH 8.5.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.028	α = 90
b = 163.482	β = 90
c = 128.826	γ = 90

Symmetry
Space Group	C 2 2 21

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		2022-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00003	SLS	X06SA

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	1.65	69.27	94.1	0.112	0.115	0.026	0.999	16.1	20.1		92187

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	1.65	1.79	59.9		2.354	2.421	0.56	0.588	1.5	18.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	64.41	1.34	92177	4605	77.31	0.1432	0.1411	0.1428	0.1826	0.1831	36.11

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	15.282
f_angle_d	1.189
f_chiral_restr	0.102
f_plane_restr	0.009
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7015
Nucleic Acid Atoms
Solvent Atoms	725
Heterogen Atoms	155

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	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.