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Structure of Apobacterioferritin Y45F variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VXI PDB ENTRY 2VXI
Crystallization Crystal Properties Matthews coefficient Solvent content 1.92 35.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.49 α = 90 b = 27.84 β = 119.18 c = 56.76 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 CCD ADSC CCD 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.39 49.56 92 0.07 8.32 2.63 26385
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 1.39 1.4 74.5 0.31 2.02 1.79
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VXI 1.392 49.557 26384 1337 91.707 0.204 0.203 0.2171 0.2249 0.2382 16.712
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] -0.546 -0.398 2.394 -0.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.056 r_dihedral_angle_4_deg 23.449 r_dihedral_angle_3_deg 14.839 r_dihedral_angle_1_deg 5.813 r_scangle_it 3.719 r_mcangle_it 2.42 r_scbond_it 2.395 r_angle_refined_deg 1.892 r_mcbond_it 1.56 r_mcbond_other 1.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.056 r_dihedral_angle_4_deg 23.449 r_dihedral_angle_3_deg 14.839 r_dihedral_angle_1_deg 5.813 r_scangle_it 3.719 r_mcangle_it 2.42 r_scbond_it 2.395 r_angle_refined_deg 1.892 r_mcbond_it 1.56 r_mcbond_other 1.548 r_angle_other_deg 0.843 r_nbd_refined 0.253 r_nbtor_refined 0.191 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.108 r_metal_ion_refined 0.081 r_symmetry_metal_ion_refined 0.059 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_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 1291 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction TRUNCATE data scaling PHASER phasing