3RGW | pdb_00003rgw

Crystal structure at 1.5 A resolution of an H2-reduced, O2-tolerant hydrogenase from Ralstonia eutropha unmasks a novel iron-sulfur cluster

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WUL	PDB ENTRY 1WUL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		282	20-30% polyethylene glycol 3350, 100 mM Bis-(2-hydroxy-ethyl)-amino-tris(hydroxymethyl)-methane buffer, pH 5.5-6.5, VAPOR DIFFUSION, SITTING DROP, temperature 282K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.091	α = 90
b = 95.646	β = 90
c = 119.145	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	ADSC QUANTUM 315r	mirrors	2010-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93950	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.5	59.57	100	0.088	0.088	11.2	6	133947	126968	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	100		0.434	0.434	3.7	5.9	19348

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WUL	1.5	59.57	126968	126968	6726	99.85	0.14035	0.14035	0.13967	0.17	0.15293	0.17	RANDOM	23.691

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]
-0.07			-0.47		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.536
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	11.299
r_dihedral_angle_1_deg	6.33
r_angle_refined_deg	1.267
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6827
Nucleic Acid Atoms
Solvent Atoms	830
Heterogen Atoms	31

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.