8W6X

Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4U9H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	283	30%(v/v) 2-methyl-2,4-pentane-d12-diol, 10 mM glucose-d12, 25 mM Tris-d11-DCl in D2O

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.705	α = 90
b = 98.485	β = 90
c = 126.86	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	RAYONIX MX225HE		2015-04-10	M	SINGLE WAVELENGTH
2	1	neutron	100	DIFFRACTOMETER	iBIX		2015-03-21	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	0.8000	SPring-8	BL26B1
2	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	1.8-5.8	JPARC MLF	BL-03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.04	50	99.9	0.059		0.062		1		19.7	8.5		397623
2	2.2	20	90.1	0.22		0.266		0.92		4.9	2.6		38335

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.04	1.07		0.461		0.496		0.924		4.1	7.2
2	2.2	2.32		0.394		0.473		0.57		2.3	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	1.04	41.69		1.34		397425	19868	99.78		0.143	0.1428	0.1474
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.2	17.94				38312	1893	88.91		0.1909	0.1893	0.2202

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	18.819
f_dihedral_angle_d	18.819
f_angle_d	1.213
f_angle_d	1.213
f_chiral_restr	0.095
f_chiral_restr	0.095
f_bond_d	0.014
f_bond_d	0.014
f_plane_restr	0.008
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6188
Nucleic Acid Atoms
Solvent Atoms	842
Heterogen Atoms	106

Software

Software
Software Name	Purpose
PHENIX	refinement
STARGazer	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.