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1.55A structure of apo bacterioferritin from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VXI PDB ENTRY 2VXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 1.8M AMMONIUM SULPHATE, 100MM ACETATE, PH 5.5
Crystal Properties Matthews coefficient Solvent content 3.47 64.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208 α = 90 b = 208 β = 90 c = 142.6 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 ADSC CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 43.2 98.4 0.1 12.8 4.1 438427 0.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 99.2 0.62 3 4.1
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 PDB ENTRY 2VXI 1.55 43.23 416504 21922 100 0.16652 0.16476 0.174 0.20007 0.2046 RANDOM 9.22
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.814 r_dihedral_angle_4_deg 22.73 r_dihedral_angle_3_deg 11.533 r_sphericity_free 6.715 r_angle_other_deg 5.565 r_dihedral_angle_1_deg 4.807 r_scangle_it 4.272 r_scbond_it 3.01 r_sphericity_bonded 2.251 r_mcangle_it 1.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.814 r_dihedral_angle_4_deg 22.73 r_dihedral_angle_3_deg 11.533 r_sphericity_free 6.715 r_angle_other_deg 5.565 r_dihedral_angle_1_deg 4.807 r_scangle_it 4.272 r_scbond_it 3.01 r_sphericity_bonded 2.251 r_mcangle_it 1.728 r_angle_refined_deg 1.649 r_rigid_bond_restr 1.449 r_mcbond_it 1.237 r_mcbond_other 0.593 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_bond_other_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15460 Nucleic Acid Atoms Solvent Atoms 2978 Heterogen Atoms 691
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing