3AYX

Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an H2-reduced condition

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1M PIPES, 15% PEG 3350, 300mM lithium sulfate, 5mM DTT, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.735	α = 90
b = 116.327	β = 91.4
c = 113.629	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	90	CCD	RAYONIX MX225HE		2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.18	20	97.6	0.08	13.6	2.9		1255206			10.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.2	98.4		0.464	2.8	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB ENTRY 1WUJ	1.18	20	1106011	1106011	59041	100	0.139	0.139		0.169	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
40	13107	15278.3

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.151
s_approx_iso_adps	0.121
s_non_zero_chiral_vol	0.103
s_zero_chiral_vol	0.102
s_similar_adp_cmpnt	0.056
s_angle_d	0.036
s_from_restr_planes	0.0313
s_bond_d	0.019
s_rigid_bond_adp_cmpnt	0.007
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13529
Nucleic Acid Atoms
Solvent Atoms	1655
Heterogen Atoms	96

Software

Software
Software Name	Purpose
BSS	data collection
MOLREP	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.