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Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 15 minutes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 30 mM cadmium nitrate, 1 M ammonium sulfate, and 200 mM sodium acetate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.471 α = 90 b = 180.471 β = 90 c = 180.471 γ = 90
Symmetry Space Group F 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 EIGER2 X 16M 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.02 90.23 100 0.09 0.094 0.02 0.999 19.8 21.6 17109 2 33.3
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 2.02 2.13 100 0.877 0.914 0.194 0.908 3.9 22
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 5LG2 2.02 63.888 17108 891 99.982 0.166 0.1648 0.1656 0.1878 0.1881 36.92
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 32.468 r_dihedral_angle_4_deg 21.05 r_dihedral_angle_3_deg 14.617 r_lrange_it 8.848 r_lrange_other 8.775 r_scangle_it 7.738 r_scangle_other 7.734 r_scbond_it 5.534 r_scbond_other 5.53 r_dihedral_angle_1_deg 5.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_4_deg 21.05 r_dihedral_angle_3_deg 14.617 r_lrange_it 8.848 r_lrange_other 8.775 r_scangle_it 7.738 r_scangle_other 7.734 r_scbond_it 5.534 r_scbond_other 5.53 r_dihedral_angle_1_deg 5.488 r_mcangle_it 4.173 r_mcangle_other 4.171 r_mcbond_other 3.26 r_mcbond_it 3.259 r_angle_other_deg 2.431 r_angle_refined_deg 1.99 r_nbd_refined 0.247 r_symmetry_nbd_refined 0.239 r_nbd_other 0.209 r_symmetry_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.131 r_metal_ion_refined 0.084 r_symmetry_nbtor_other 0.075 r_bond_other_d 0.035 r_symmetry_metal_ion_refined 0.019 r_bond_refined_d 0.015 r_gen_planes_other 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1355 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing