9R5I | pdb_00009r5i

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3

X-RAY DIFFRACTION

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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	6.5	293.15	The enzyme was crystallized at a concentration of 38.8 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, and 2 mM dithiothreitol. Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3 %) atmosphere by initial screening at 20 degrees Celsius using the sitting-drop method on 96-well MRC two-drop crystallisation plates in polystyrene (SWISSCI). The reservoir contained 90 ul of the following crystallization solution: 30 % (v/v) Polyethylene glycol 400, 100 mM MES pH 6.5, and 200 mM LiSO4. 0.7 ul of protein and 0.7 ul of the crystallization solution were spotted.

Crystal Properties
Matthews coefficient	Solvent content
5.34	76.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.606	α = 90
b = 196.606	β = 90
c = 192.072	γ = 120

Symmetry
Space Group	P 31 2 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	1.73891	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	3.13	127.41	95.1	0.304	0.312	0.069	0.997	10	20.2		52281

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	3.13	3.35	67.7		2.449	2.51	0.545	0.62	1.6	21.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.13	77.83	1.34	52264	2614	69.02	0.176	0.1744	0.175	0.2059	0.204	Random selection	82.44

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	15.613
f_angle_d	0.935
f_chiral_restr	0.077
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14094
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	389

Software

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