3ZEA

3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the reduced state at 1.82 Angstroms

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WPN	PDB ENTRY 2WPN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.1		CRYSTALS WERE OBTAINED USING THE SITTING-DROP VAPOR DIFFUSION METHOD. 1 UL OF A RESERVOIR SOLUTION CONTAINING 16% PEG 8000 (W/V) AND 0.05 M KH2PO4 PH 4.1 WAS MIXED WITH AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 11 MG/ML PROTEIN IN 20 MM TRIS-HCL BUFFER PH 7.6, AND EQUILIBRATED AGAINST A 500 UL RESERVOIR.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.796	α = 90
b = 61.796	β = 90
c = 339.297	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 PILATUS 6M		2011-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	1.82	56.6	97.7	0.04	23.3	4.1		67904

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	1.82	1.93	89.9		0.08	9.3	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PDB ENTRY 2WPN	1.82	56.55	1.4	67701	5689	86.13	0.1249	0.1238	0.14	0.1468	0.16

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]
0.6664			0.6664		-1.3328

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.257
f_angle_d	1.251
f_chiral_restr	0.074
f_bond_d	0.01
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5838
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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.