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Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron flavoprotein, inactive oxidized state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other based on 2.8 A structure of rubredoxin:NO/O2 oxidoreductase from Mo. 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 2.45 49.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.7 α = 90 b = 88.7 β = 90 c = 450.4 γ = 90
Symmetry Space Group P 43 21 2
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 2006-10-04 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 2.26 48.11 97.2 6.3 16.7 4.5 80298 80298
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 2.26 2.32 74 7.1 2.4
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 FprA 2.26 48.11 80298 80298 4222 99 0.18844 0.18844 0.1861 0.1866 0.23381 0.2355 RANDOM 24.862
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] 0.07 0.07 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.848 r_dihedral_angle_4_deg 17.433 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_1_deg 6.172 r_scangle_it 2.412 r_scbond_it 1.503 r_angle_refined_deg 1.299 r_mcangle_it 0.926 r_mcbond_it 0.533 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.848 r_dihedral_angle_4_deg 17.433 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_1_deg 6.172 r_scangle_it 2.412 r_scbond_it 1.503 r_angle_refined_deg 1.299 r_mcangle_it 0.926 r_mcbond_it 0.533 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.155 r_symmetry_metal_ion_refined 0.135 r_symmetry_hbond_refined 0.11 r_metal_ion_refined 0.098 r_chiral_restr 0.09 r_bond_refined_d 0.011 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_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 Atoms Number Protein Atoms 12648 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection XDS data reduction XDS data scaling EPMR phasing