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Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 15 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 3.7 66.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.907 α = 90 b = 151.907 β = 90 c = 151.907 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 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 2.3 48.04 100 0.086 0.091 0.02 1 23.9 21.3 13632 2 47.7
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 2.3 2.42 100 1.041 1.089 0.232 0.901 3.3 21.7
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 2.3 43.89 13623 670 99.956 0.198 0.1952 0.1953 0.2623 0.2626 47.514
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 35.853 r_dihedral_angle_4_deg 25.931 r_dihedral_angle_3_deg 16.699 r_lrange_it 12.232 r_lrange_other 12.212 r_scangle_it 10.182 r_scangle_other 10.182 r_scbond_it 7.266 r_scbond_other 7.261 r_mcangle_it 6.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.853 r_dihedral_angle_4_deg 25.931 r_dihedral_angle_3_deg 16.699 r_lrange_it 12.232 r_lrange_other 12.212 r_scangle_it 10.182 r_scangle_other 10.182 r_scbond_it 7.266 r_scbond_other 7.261 r_mcangle_it 6.25 r_mcangle_other 6.247 r_dihedral_angle_1_deg 5.581 r_mcbond_other 4.5 r_mcbond_it 4.499 r_angle_other_deg 2.479 r_angle_refined_deg 1.909 r_nbd_refined 0.241 r_nbd_other 0.237 r_symmetry_nbd_other 0.223 r_nbtor_refined 0.185 r_chiral_restr 0.182 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.101 r_metal_ion_refined 0.08 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.036 r_symmetry_metal_ion_refined 0.019 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 1380 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing