1FRF | pdb_00001frf

CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.4		PEG 6000 28%, MES 100MM PH 6,4 25MM OCTYL-BETA-D-GLUCOPYRANOSIDE, pH 6.4

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.61	α = 90
b = 99.77	β = 90.88
c = 184.51	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	110			MIRRORS	1996-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM02		ESRF	BM02

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	2.7	38.7	66.7	0.061	10.2	2.8		43607		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.77	56.4		0.32	2	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1FRV	2.7	12	2	32894		66.7	0.2201	0.22	0.274	RANDOM	12.48

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	24.41
x_angle_deg	1.962
x_improper_angle_d	1.63
x_bond_d	0.014
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6138
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XDS	data scaling
CCP4	data reduction
AMoRE	phasing
X-PLOR	refinement
XDS	data reduction
CCP4	data scaling