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Crystal structure of E. coli Bacterioferritin (BFR) soaked in phosphate with an alternative conformation of the unoccupied Ferroxidase centre (APO-BFR II).
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 AMMOMIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. SUBSEQUENTLY, THE CRYSTALS WERE SOAKED IN A CRYO-PROTECTANT BUFFER CONTAINING PHOSPHATE BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00
Crystal Properties Matthews coefficient Solvent content 3.49 64.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.082 α = 90 b = 208.082 β = 90 c = 143.107 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 2.5 34.2 96.4 0.101 19.6 13.9 104275 1
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) 2.5 2.64 80.7 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 2.5 34 99059 5157 96.2 0.236 0.236 0.2314 0.248 0.2441 EXTENDED FROM THE VALIDATION SET USED IN 2QP7. 11.67
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] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.119 r_dihedral_angle_4_deg 24.406 r_dihedral_angle_3_deg 20.307 r_dihedral_angle_1_deg 4.248 r_scangle_it 3.493 r_scbond_it 2.237 r_angle_refined_deg 1.368 r_mcangle_it 1.122 r_mcbond_it 0.728 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.119 r_dihedral_angle_4_deg 24.406 r_dihedral_angle_3_deg 20.307 r_dihedral_angle_1_deg 4.248 r_scangle_it 3.493 r_scbond_it 2.237 r_angle_refined_deg 1.368 r_mcangle_it 1.122 r_mcbond_it 0.728 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.123 r_bond_refined_d 0.012 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_refined 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 15876 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 337
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling