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A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein from Bacteroides fragilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CLB PDB ENTRY 2CLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M BIS-TRIS HCL PH 8.5, 0.25 M MGCL2, 16 % (W/V) PEG 4,000, 2 % (W/V) BENZAMIDINE HCL, 20 % GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.695 α = 90 b = 129.695 β = 90 c = 129.695 γ = 90
Symmetry Space Group P 21 3
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 2007-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.3 37 99.6 0.08 17.5 3.6 34431 2
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 2.3 2.38 99.4 0.24 2.9 1.9
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 PDB ENTRY 2CLB 2.3 37 30759 1629 99.5 0.197 0.195 0.198 0.224 0.2245 RANDOM 34.86
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.984 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 4.684 r_angle_other_deg 2.52 r_scangle_it 2.155 r_scbond_it 1.527 r_angle_refined_deg 1.152 r_mcangle_it 0.847 r_mcbond_it 0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.984 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 4.684 r_angle_other_deg 2.52 r_scangle_it 2.155 r_scbond_it 1.527 r_angle_refined_deg 1.152 r_mcangle_it 0.847 r_mcbond_it 0.842 r_symmetry_vdw_other 0.315 r_nbd_refined 0.222 r_nbd_other 0.203 r_symmetry_vdw_refined 0.177 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.168 r_nbtor_other 0.083 r_chiral_restr 0.063 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5413 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling COMO phasing