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Crystal structure of human L ferritin (HuLf) 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 3.59 65.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.14 α = 90 b = 151.14 β = 90 c = 151.14 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 1.73891 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 1 2.09 106.87 93.5 0.065 0.069 0.015 1 26.8 20.3 16631 2 42.6
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 2.09 2.2 100 0.849 0.887 0.19 0.925 3.7 21.5
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 2.09 47.84 16500 823 92.848 0.211 0.2087 0.2088 0.252 0.2522 44.84
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 37.38 r_dihedral_angle_4_deg 25.739 r_dihedral_angle_3_deg 17.642 r_lrange_it 11.001 r_lrange_other 10.848 r_scangle_it 8.946 r_scangle_other 8.945 r_scbond_it 6.323 r_scbond_other 6.319 r_dihedral_angle_1_deg 5.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.38 r_dihedral_angle_4_deg 25.739 r_dihedral_angle_3_deg 17.642 r_lrange_it 11.001 r_lrange_other 10.848 r_scangle_it 8.946 r_scangle_other 8.945 r_scbond_it 6.323 r_scbond_other 6.319 r_dihedral_angle_1_deg 5.857 r_mcangle_it 5.556 r_mcangle_other 5.552 r_mcbond_it 4.231 r_mcbond_other 4.187 r_angle_other_deg 2.439 r_angle_refined_deg 1.858 r_nbd_other 0.262 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.252 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.17 r_symmetry_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.104 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.036 r_bond_refined_d 0.014 r_gen_planes_other 0.01 r_symmetry_xyhbond_nbd_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1382 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing