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Crystal structure of E. coli Bacterioferritin (BFR) in which the Ferroxidase centre is inhibited with ZN(II) and high occupancy iron is bound within the cavity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QP7 2QP7 (APO-BFR)
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. APO-BFR CRYSTALS WERE SUBSEQUENTLY (AEROBICALLY) SOAKED IN A CRYOPROTECTANT SOLUTION CONTAINING FE2+ (AND BUFFERED AT PH 7.0 WITH 0.1 M MOPS IN PLACE OF CITRATE) FOR 65 MINUTES BEFORE FALSH FREEZING AND DATA COLLECTION. PLEASE SEE PAPER FOR FULL DETAILS., PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.397 α = 90 b = 207.397 β = 90 c = 142.451 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 2.4 73.32 97 0.116 16.3 12 117098
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) 2.4 2.53 83.3 0.372 3.1 3.9
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 (APO-BFR) 2.4 71.25 111243 5788 96.8 0.241 0.24 0.2361 0.26 0.2552 EXTENDED FROM 2QP7 13.33
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] -0.26 -0.26 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.474 r_dihedral_angle_4_deg 20.848 r_dihedral_angle_3_deg 18.09 r_dihedral_angle_1_deg 5.081 r_scangle_it 3.304 r_scbond_it 2.079 r_angle_refined_deg 1.433 r_mcangle_it 1.073 r_mcbond_it 0.767 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.474 r_dihedral_angle_4_deg 20.848 r_dihedral_angle_3_deg 18.09 r_dihedral_angle_1_deg 5.081 r_scangle_it 3.304 r_scbond_it 2.079 r_angle_refined_deg 1.433 r_mcangle_it 1.073 r_mcbond_it 0.767 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.127 r_metal_ion_refined 0.05 r_bond_refined_d 0.012 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_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 15792 Nucleic Acid Atoms Solvent Atoms 863 Heterogen Atoms 374
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling