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Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A
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 66.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.215 α = 90 b = 151.215 β = 90 c = 151.215 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 2018-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2.46 75.61 100 0.106 0.112 0.024 1 21.2 21.2 11055 2 50.2
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 2.46 2.59 100 1.044 1.09 0.233 0.929 3.1 21.6
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 2.46 61.81 10926 581 98.869 0.204 0.2005 0.2004 0.2579 0.2581 47.624
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 35.271 r_dihedral_angle_4_deg 23.051 r_dihedral_angle_3_deg 16.807 r_lrange_it 9.876 r_lrange_other 9.819 r_scangle_it 8.237 r_scangle_other 8.234 r_mcangle_other 6.152 r_mcangle_it 6.148 r_scbond_it 5.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.271 r_dihedral_angle_4_deg 23.051 r_dihedral_angle_3_deg 16.807 r_lrange_it 9.876 r_lrange_other 9.819 r_scangle_it 8.237 r_scangle_other 8.234 r_mcangle_other 6.152 r_mcangle_it 6.148 r_scbond_it 5.834 r_scbond_other 5.83 r_dihedral_angle_1_deg 5.801 r_mcbond_it 4.35 r_mcbond_other 4.339 r_angle_other_deg 2.465 r_angle_refined_deg 1.751 r_symmetry_nbd_refined 0.257 r_metal_ion_refined 0.245 r_nbd_refined 0.229 r_symmetry_metal_ion_refined 0.224 r_symmetry_nbd_other 0.221 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_other 0.208 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.188 r_nbtor_refined 0.184 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.036 r_bond_refined_d 0.014 r_gen_planes_other 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1364 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing