9R6Z | pdb_00009r6z

Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus

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	7.5	293.15	The enzyme used for crystallisation was concentrated at 16 mg/ml in a buffer containing 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, 2 mM dithiothreitol and 2 mM FAD. Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3 %) atmosphere by initial screening at 20 degree Celsius using the sitting-drop method on 96-well MRC two-drop crystallisation plates in polystyrene (SWISSCI) containing 90 ul of crystallisation solution in the reservoir. The crystallisation solution was 1.5 M LiSO4 and 100 mM HEPES pH 7.5. Prior to freezing, the crystal was soaked in the crystallisation solution supplemented with 30% (v/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
4.66	73.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 282.072	α = 90
b = 282.072	β = 90
c = 282.072	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2016-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	1.3871	ESRF	BM30A

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	2.85	49.1	100	0.217	0.233	0.085	0.988	6	7.6		173025

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	2.85	3	100		1.497	1.605	0.572	0.433	1.2	7.8

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	2.85	31.34	1.33	172727	8753	99.91	0.1837	0.1823	0.1831	0.2101	0.2105	Random selection	82

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	16.034
f_angle_d	0.878
f_chiral_restr	0.056
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28188
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	562

Software

Software
Software Name	Purpose
PHENIX	refinement
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	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.