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The structure of Mycobacterial bacterioferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 100mM HEPES pH 7.5, 10% (v/v) 2-propanol, 14% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.85 56.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.523 α = 90 b = 151.52 β = 128.08 c = 116.715 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH Si(111) monochromator 2007-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.905 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.72 30 99.4 0.11 0.11 10 2.7 65786 65786 43.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.76 99.8 0.528 0.528 2.3 2.7 3302
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1sof 2.72 29.64 63129 63129 2649 98.78 0.18144 0.18144 0.17947 0.1857 0.22828 0.2326 RANDOM 46.756
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] 0.35 -0.71 -0.24 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.277 r_dihedral_angle_4_deg 22.701 r_dihedral_angle_3_deg 18.814 r_dihedral_angle_1_deg 4.646 r_scangle_it 3.03 r_scbond_it 1.752 r_angle_refined_deg 1.715 r_mcangle_it 1.695 r_mcbond_it 1.028 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.277 r_dihedral_angle_4_deg 22.701 r_dihedral_angle_3_deg 18.814 r_dihedral_angle_1_deg 4.646 r_scangle_it 3.03 r_scbond_it 1.752 r_angle_refined_deg 1.715 r_mcangle_it 1.695 r_mcbond_it 1.028 r_nbtor_refined 0.313 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.226 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.121 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15564 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 367
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing