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Crystal structure of E. coli Bacterioferritin (BFR) after a 65 minute (aerobic) exposure to FE(II) revealing a possible MU-OXO bridge/MU-Hydroxy bridged DIIRON intermediate at the ferroxidase centre. (FE(III)-O-FE(III)-BFR).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. CRYSTALS OF OF APO-BFR WERE SUBSEQUENTLY SOAKED AEROBICALLY FOR 65 MINUTES IN A SOLUTION CONTAINING FE2+ AND BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE PH 5. AFTER 65MIN EXPOSURE TO IRON AND AIR, THE CRYSTAL WAS FLASH FROZEN IN LIQUID NITROGEN AND X-RAY DIFFRACTION DATA COLLECTED. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00
Crystal Properties Matthews coefficient Solvent content 3.47 64.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.741 α = 90 b = 207.741 β = 90 c = 142.951 γ = 90
Symmetry Space Group P 42 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 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 2.8 32.7 98.1 0.17 13.6 11 75629
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) 2.8 2.95 91.9 0.251 5.2 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2QP7 2.8 32.67 71794 3785 98 0.251 0.25 0.2453 0.268 0.2613 EXTENDED FROM THE SAME SET USED IN 2QP7 (APO-BFR) 10.82
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] -0.74 -0.74 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.238 r_dihedral_angle_3_deg 21.763 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_1_deg 4.891 r_scangle_it 3.482 r_scbond_it 2.186 r_angle_refined_deg 1.856 r_mcangle_it 1.208 r_mcbond_it 0.819 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.238 r_dihedral_angle_3_deg 21.763 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_1_deg 4.891 r_scangle_it 3.482 r_scbond_it 2.186 r_angle_refined_deg 1.856 r_mcangle_it 1.208 r_mcbond_it 0.819 r_nbtor_refined 0.32 r_symmetry_hbond_refined 0.309 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.149 r_metal_ion_refined 0.048 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 15912 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 374
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling