3H3X | pdb_00003h3x

Structure of the V74M large subunit mutant of NI-FE hydrogenase in an oxidized state

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG6000, GLYCEROL, pH6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.4	α = 90
b = 99.2	β = 92.8
c = 182.3	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r	mirrors	2008-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97623	ESRF	ID29

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	2.7	20	98.7	0.051	0.051	15.18	3.42	61024	60250			42.6

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	2.7	2.8	98.1		0.288	0.288	4.31	3.07	6288

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 (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 1YQW	2.7	20	60250	57315	2935	98.73	0.206	0.203	0.21	0.247	0.25	RANDOM	41.52

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]
2.17		2.44	-0.96		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.532
r_dihedral_angle_4_deg	15.862
r_dihedral_angle_3_deg	15.823
r_dihedral_angle_1_deg	6.013
r_scangle_it	1.541
r_angle_refined_deg	1.451
r_scbond_it	1.054
r_mcangle_it	0.563
r_mcbond_it	0.367
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.286
r_symmetry_vdw_refined	0.242
r_metal_ion_refined	0.211
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18400
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	138

Software

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