2OHJ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherbased on 2.8 A structure of rubredoxin:NO/O2 oxidoreductase from Mo. thermoacetica

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52830.001M 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 coefficientSolvent content
2.4549.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.7α = 90
b = 88.7β = 90
c = 450.4γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2006-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2648.1197.26.316.74.58029880298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.32747.12.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTFprA2.2648.1180298802984222990.188440.188440.18610.23381RANDOM24.862
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]
0.070.07-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.848
r_dihedral_angle_4_deg17.433
r_dihedral_angle_3_deg15.922
r_dihedral_angle_1_deg6.172
r_scangle_it2.412
r_scbond_it1.503
r_angle_refined_deg1.299
r_mcangle_it0.926
r_mcbond_it0.533
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.848
r_dihedral_angle_4_deg17.433
r_dihedral_angle_3_deg15.922
r_dihedral_angle_1_deg6.172
r_scangle_it2.412
r_scbond_it1.503
r_angle_refined_deg1.299
r_mcangle_it0.926
r_mcbond_it0.533
r_nbtor_refined0.302
r_symmetry_vdw_refined0.233
r_nbd_refined0.197
r_xyhbond_nbd_refined0.155
r_symmetry_metal_ion_refined0.135
r_symmetry_hbond_refined0.11
r_metal_ion_refined0.098
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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 AtomsNumber
Protein Atoms12648
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
EPMRphasing