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Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A Fe(III)-loaded for 60 minutes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.69 66.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.222 α = 90 b = 151.222 β = 90 c = 151.222 γ = 90
Symmetry Space Group I 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 PILATUS3 6M 2018-02-19 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-02-19 M MAD 3 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-02-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I03 1.73888 Diamond I03 3 SYNCHROTRON DIAMOND BEAMLINE I03 1.74478 Diamond I03
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 2 2.18 47.94 100 0.094 0.106 0.023 1 18.6 20.5 15856 2 55
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) 2 2.18 2.3 100 1.589 1.668 0.371 0.722 2.1 20
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 5LG8 2.2 53.522 15290 761 99.772 0.198 0.1958 0.1959 0.238 0.2378 44.781
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 35.378 r_dihedral_angle_4_deg 23.53 r_dihedral_angle_3_deg 16.711 r_lrange_other 12.063 r_lrange_it 12.059 r_scangle_it 9.997 r_scangle_other 9.993 r_scbond_it 7.127 r_scbond_other 7.122 r_mcangle_other 6.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 23.53 r_dihedral_angle_3_deg 16.711 r_lrange_other 12.063 r_lrange_it 12.059 r_scangle_it 9.997 r_scangle_other 9.993 r_scbond_it 7.127 r_scbond_other 7.122 r_mcangle_other 6.567 r_mcangle_it 6.536 r_dihedral_angle_1_deg 5.949 r_mcbond_it 4.775 r_mcbond_other 4.574 r_angle_other_deg 2.537 r_angle_refined_deg 1.987 r_symmetry_nbd_refined 0.293 r_nbd_refined 0.249 r_symmetry_nbd_other 0.22 r_nbd_other 0.215 r_chiral_restr 0.193 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.159 r_metal_ion_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_metal_ion_refined 0.137 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1364 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing