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Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A Fe(III)-loaded for 30 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 3.73 66.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.386 α = 90 b = 151.386 β = 90 c = 151.386 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 2.18 107.34 100 0.088 0.101 0.022 1 21.2 20.1 15908 2 55.9
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 1.513 1.585 0.351 0.744 2.2 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 47.918 15218 755 98.985 0.206 0.2035 0.2033 0.2481 0.2483 44.069
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 33.928 r_dihedral_angle_4_deg 24.618 r_dihedral_angle_3_deg 16.076 r_lrange_other 11.424 r_lrange_it 11.418 r_scangle_it 8.915 r_scangle_other 8.915 r_scbond_it 6.478 r_scbond_other 6.473 r_dihedral_angle_1_deg 5.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_4_deg 24.618 r_dihedral_angle_3_deg 16.076 r_lrange_other 11.424 r_lrange_it 11.418 r_scangle_it 8.915 r_scangle_other 8.915 r_scbond_it 6.478 r_scbond_other 6.473 r_dihedral_angle_1_deg 5.909 r_mcangle_it 5.703 r_mcangle_other 5.703 r_mcbond_it 4.392 r_mcbond_other 4.371 r_angle_other_deg 2.471 r_angle_refined_deg 1.875 r_nbd_other 0.258 r_nbd_refined 0.241 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.189 r_chiral_restr 0.174 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.14 r_metal_ion_refined 0.139 r_symmetry_metal_ion_refined 0.122 r_symmetry_nbtor_other 0.076 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 1352 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing