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Structure of Apobacterioferritin
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 1.93 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.97 α = 90 b = 28.3 β = 103.48 c = 54.47 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 2.1 46.66 99 0.06 11.16 2.63 8475
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 2.1 2.15 99.5 0.43 1.81 2.66
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 2.11 46.64 7929 386 98.27 0.21938 0.21573 0.2247 0.29877 0.2206 RANDOM 37.524
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] -2.17 0.08 6.06 -3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.564 r_dihedral_angle_4_deg 17.086 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_1_deg 6.323 r_mcangle_it 4.409 r_scbond_it 3.104 r_mcbond_it 2.641 r_mcbond_other 2.637 r_angle_refined_deg 1.484 r_angle_other_deg 1.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.564 r_dihedral_angle_4_deg 17.086 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_1_deg 6.323 r_mcangle_it 4.409 r_scbond_it 3.104 r_mcbond_it 2.641 r_mcbond_other 2.637 r_angle_refined_deg 1.484 r_angle_other_deg 1.032 r_chiral_restr 0.179 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it 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 1272 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing