2OHI

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


X-RAY DIFFRACTION

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
2.244.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.798α = 90
b = 123.113β = 103.4
c = 135.864γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCDmirrors2006-04-27MSINGLE 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
12.32097.66.613.72.6103861103861
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3597.836.41.82.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.320103861103861553078.870.20610.202810.26907RANDOM43.975
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]
1.85-1.61-1.39-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.345
r_dihedral_angle_3_deg18.759
r_dihedral_angle_4_deg18.62
r_dihedral_angle_1_deg5.908
r_scangle_it1.914
r_angle_refined_deg1.363
r_scbond_it1.221
r_mcangle_it0.811
r_mcbond_it0.457
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.345
r_dihedral_angle_3_deg18.759
r_dihedral_angle_4_deg18.62
r_dihedral_angle_1_deg5.908
r_scangle_it1.914
r_angle_refined_deg1.363
r_scbond_it1.221
r_mcangle_it0.811
r_mcbond_it0.457
r_nbtor_refined0.305
r_symmetry_vdw_refined0.217
r_nbd_refined0.205
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.141
r_chiral_restr0.095
r_metal_ion_refined0.037
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_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 AtomsNumber
Protein Atoms25296
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms268

Software

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