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Crystal structure of human L ferritin (HuLf) 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 3.76 67.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.69 α = 90 b = 152.69 β = 90 c = 152.69 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 PILATUS 6M-F 2017-12-12 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-12-12 M MAD 3 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-12-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 ESRF ID29 2 SYNCHROTRON ESRF BEAMLINE ID29 1.73769 ESRF ID29 3 SYNCHROTRON ESRF BEAMLINE ID29 1.74502 ESRF ID29
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 48.28 100 0.122 0.128 0.028 0.999 13.6 21.3 16176 2 47.2
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 1.573 1.641 0.347 0.839 2.2 22.1
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 2.18 48.28 16074 825 99.369 0.205 0.2021 0.2022 0.2575 0.2582 47.655
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 34.428 r_dihedral_angle_4_deg 24.294 r_dihedral_angle_3_deg 17.05 r_lrange_it 11.01 r_lrange_other 10.855 r_scangle_other 9.196 r_scangle_it 9.191 r_scbond_it 6.99 r_scbond_other 6.985 r_mcangle_other 6.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 24.294 r_dihedral_angle_3_deg 17.05 r_lrange_it 11.01 r_lrange_other 10.855 r_scangle_other 9.196 r_scangle_it 9.191 r_scbond_it 6.99 r_scbond_other 6.985 r_mcangle_other 6.228 r_mcangle_it 6.223 r_dihedral_angle_1_deg 5.564 r_mcbond_it 4.641 r_mcbond_other 4.615 r_angle_other_deg 2.445 r_angle_refined_deg 1.796 r_symmetry_nbd_refined 0.33 r_nbd_refined 0.246 r_symmetry_xyhbond_nbd_refined 0.229 r_symmetry_nbd_other 0.212 r_nbd_other 0.191 r_nbtor_refined 0.187 r_chiral_restr 0.174 r_xyhbond_nbd_refined 0.171 r_metal_ion_refined 0.119 r_symmetry_nbtor_other 0.075 r_bond_other_d 0.036 r_bond_refined_d 0.014 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1376 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing