2OHH | pdb_00002ohh

Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron flavoprotein, active oxidized state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Rugredoxin:NO/NO2 oxidoreductase from Moorella thermoacetica

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	283	0.001M DDT, 0.2M ammonium sulfate, 0.1M MES/KOH, 30% PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.74	α = 90
b = 120.86	β = 110.4
c = 92.69	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	MARMOSAIC 225 mm CCD	mirrors	2005-06-24	M	SINGLE WAVELENGTH

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

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	1.7	10	99.2	7.8	9.9	4.6	156544	156544

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	1.7	1.77	98.9		2.3	2.1

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-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	Rugredoxin:NO/NO2 oxidoreductase from Moorella thermoacetica	1.7	10	156544	156544	8277	99.31	0.18595	0.18595	0.18424	0.1843	0.21843	0.2214	RANDOM	33.07

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]
-1.1		0.56	1.91		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.17
r_dihedral_angle_4_deg	16.7
r_dihedral_angle_3_deg	15.349
r_dihedral_angle_1_deg	8.962
r_scangle_it	3.957
r_scbond_it	2.724
r_angle_refined_deg	1.871
r_mcangle_it	1.54
r_mcbond_it	1.157
r_nbtor_refined	0.328
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.194
r_symmetry_hbond_refined	0.184
r_chiral_restr	0.121
r_metal_ion_refined	0.101
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12648
Nucleic Acid Atoms
Solvent Atoms	925
Heterogen Atoms	137

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
XDS	data scaling
EPMR	phasing