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Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 60 minutes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 30 mM cadmium nitrate, 1 M ammonium sulfate, 200 mM sodium acetate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.2 61.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.281 α = 90 b = 181.281 β = 90 c = 181.281 γ = 90
Symmetry Space Group F 4 3 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 PIXEL DECTRIS EIGER2 X 16M 2019-07-26 M MAD 2 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2019-07-26 M MAD 3 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2019-07-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04 2 SYNCHROTRON DIAMOND BEAMLINE I04 1.73892 Diamond I04 3 SYNCHROTRON DIAMOND BEAMLINE I04 1.75120 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.18 104.66 100 0.084 0.089 0.019 1 21.8 21.6 13865 2 45.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.3 100 1.092 1.138 0.241 0.863 3.3 22
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5LG2 2.18 104.66 13862 696 99.964 0.2 0.1969 0.1968 0.2567 0.257 45.412
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 33.901 r_dihedral_angle_4_deg 22.134 r_dihedral_angle_3_deg 16.226 r_lrange_it 11.384 r_lrange_other 11.157 r_scangle_it 9.38 r_scangle_other 9.375 r_scbond_it 6.713 r_scbond_other 6.708 r_dihedral_angle_1_deg 5.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.901 r_dihedral_angle_4_deg 22.134 r_dihedral_angle_3_deg 16.226 r_lrange_it 11.384 r_lrange_other 11.157 r_scangle_it 9.38 r_scangle_other 9.375 r_scbond_it 6.713 r_scbond_other 6.708 r_dihedral_angle_1_deg 5.491 r_mcangle_it 5.241 r_mcangle_other 5.239 r_mcbond_other 3.904 r_mcbond_it 3.903 r_angle_other_deg 2.393 r_angle_refined_deg 1.764 r_nbd_refined 0.236 r_symmetry_nbd_other 0.211 r_symmetry_nbd_refined 0.202 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.158 r_chiral_restr 0.146 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.077 r_bond_other_d 0.035 r_bond_refined_d 0.014 r_gen_planes_other 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1339 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing