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Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 30 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, 200 mM sodium acetate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.242 α = 90 b = 181.242 β = 90 c = 181.242 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 2019-07-26 M MAD 2 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2019-07-26 M MAD 3 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2019-07-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04 2 SYNCHROTRON DIAMOND BEAMLINE I04 1.73894 Diamond I04 3 SYNCHROTRON DIAMOND BEAMLINE I04 1.75120 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 2.02 104.64 100 0.056 0.06 0.013 1 30.4 21.7 17298 2 38.7
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 2.02 2.13 100 0.901 0.941 0.199 0.915 3.9 22.2
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 2.021 54.706 17294 900 99.971 0.186 0.1844 0.1845 0.2211 0.2211 41.696
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 32.853 r_dihedral_angle_4_deg 18.835 r_dihedral_angle_3_deg 15.599 r_lrange_it 10.183 r_lrange_other 9.866 r_scangle_it 9.189 r_scangle_other 9.184 r_scbond_it 6.466 r_scbond_other 6.462 r_dihedral_angle_1_deg 5.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_4_deg 18.835 r_dihedral_angle_3_deg 15.599 r_lrange_it 10.183 r_lrange_other 9.866 r_scangle_it 9.189 r_scangle_other 9.184 r_scbond_it 6.466 r_scbond_other 6.462 r_dihedral_angle_1_deg 5.16 r_mcangle_it 4.211 r_mcangle_other 4.208 r_mcbond_other 3.477 r_mcbond_it 3.474 r_angle_other_deg 2.4 r_angle_refined_deg 1.907 r_nbd_refined 0.246 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.184 r_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.15 r_symmetry_nbd_refined 0.146 r_chiral_restr 0.132 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.036 r_bond_refined_d 0.014 r_gen_planes_other 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1348 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing