2B0J

The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	283	Hepes/NaOH, 2-propanol, PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.37	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.47	α = 90
b = 59.88	β = 90
c = 68.49	γ = 90

Symmetry
Space Group	P 21 21 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		2005-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97858	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	40	99.6	0.075	14.1	3.8	38541	38541

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	1.795	99.8		0.64	2.5	4	2820

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	structure of Hmd from Methanopyrus kandleri	1.75	40	38541	36576	1933	99.59	0.193	0.19146	0.21679	RANDOM	32.395

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]
-1.2			0.09		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.716
r_dihedral_angle_4_deg	23.446
r_dihedral_angle_3_deg	17.206
r_dihedral_angle_1_deg	5.059
r_scangle_it	3.995
r_scbond_it	2.558
r_angle_refined_deg	1.54
r_mcangle_it	1.411
r_mcbond_it	0.959
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.716
r_dihedral_angle_4_deg	23.446
r_dihedral_angle_3_deg	17.206
r_dihedral_angle_1_deg	5.059
r_scangle_it	3.995
r_scbond_it	2.558
r_angle_refined_deg	1.54
r_mcangle_it	1.411
r_mcbond_it	0.959
r_nbtor_refined	0.312
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2593
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
EPMR	phasing

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.