1YQ9

Structure of the unready oxidized form of [NiFe] hydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.3	293	PEG8000, sodium chloride, N,N-dimethyl dodecylamine N-oxide, glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.75	α = 89.33
b = 93.44	β = 102.41
c = 69.03	γ = 90.95

Symmetry
Space Group	P 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	IMAGE PLATE	MARRESEARCH		1996-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.35	19.8	86.2	0.069	8.4	1.8		58639			37.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.45	78.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2FRV	2.35	13	61447	58485	2962	92.2	0.135	0.132	0.183	RANDOM	14.54

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]
2.37	-1.11	0.02	0.13	0.9	-2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.337
r_dihedral_angle_4_deg	19.189
r_dihedral_angle_3_deg	17.933
r_dihedral_angle_1_deg	5.397
r_scangle_it	2.52
r_scbond_it	1.969
r_mcangle_it	1.473
r_mcbond_it	1.157
r_angle_refined_deg	1.088
r_nbtor_refined	0.324
r_symmetry_hbond_refined	0.282
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.158
r_symmetry_vdw_refined	0.158
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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_refined
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	12237
Nucleic Acid Atoms
Solvent Atoms	515
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
XDS	data scaling
AMoRE	phasing