3F47

The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	283	50% MPD, 100mM Tris-HCl, 20mM Ammonium dihydrogen phosphate, 1mM DTT , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.93	α = 90
b = 95.93	β = 90
c = 165.81	γ = 90

Symmetry
Space Group	I 41 2 2

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	MARMOSAIC 225 mm CCD	Dynamically bendable mirror	2007-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9920	SLS	X10SA

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	1.75	26.2	95.5	0.056	16	5.2		37583		-3	32.677

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	1.75	1.8	81.6		0.508	2.6	3.6	9296

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3DAG	1.75	25	37574	1887	95.63	0.174	0.173	0.205	RANDOM	33.553

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]
0.82			0.82		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.713
r_dihedral_angle_4_deg	21.905
r_dihedral_angle_3_deg	13.397
r_dihedral_angle_1_deg	5.255
r_scangle_it	3.978
r_scbond_it	2.474
r_angle_refined_deg	1.578
r_mcangle_it	1.294
r_mcbond_it	0.749
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.713
r_dihedral_angle_4_deg	21.905
r_dihedral_angle_3_deg	13.397
r_dihedral_angle_1_deg	5.255
r_scangle_it	3.978
r_scbond_it	2.474
r_angle_refined_deg	1.578
r_mcangle_it	1.294
r_mcbond_it	0.749
r_nbtor_refined	0.302
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2593
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
REFMAC	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.