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X-ray structure of Ru(bpy)3]2+ complex (Ru1)-encapsulated human heavy chain ferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.0 M magnesium chloride, 0.1 M bicine buffer pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.77 α = 90 b = 183.77 β = 90 c = 183.77 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 PILATUS 6M 2022-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
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 1.57 106.1 99.4 0.2 0.25 0.03 0.998 15 20 37411
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 1.57 1.59 100 1 0.9 0.38 0.846 15
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 FREE R-VALUE 5n27 1.57 105.622 37338 1879 99.245 0.162 0.1602 0.1729 0.1904 0.2027 21.802
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 39.155 r_dihedral_angle_4_deg 23.09 r_dihedral_angle_3_deg 12.522 r_lrange_it 7.488 r_lrange_other 6.984 r_dihedral_angle_1_deg 5.612 r_scangle_it 5.597 r_scangle_other 5.597 r_scbond_it 3.691 r_scbond_other 3.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.155 r_dihedral_angle_4_deg 23.09 r_dihedral_angle_3_deg 12.522 r_lrange_it 7.488 r_lrange_other 6.984 r_dihedral_angle_1_deg 5.612 r_scangle_it 5.597 r_scangle_other 5.597 r_scbond_it 3.691 r_scbond_other 3.689 r_mcangle_it 3.296 r_mcangle_other 3.28 r_mcbond_it 2.097 r_mcbond_other 2.076 r_angle_refined_deg 1.774 r_angle_other_deg 1.574 r_symmetry_xyhbond_nbd_refined 0.324 r_xyhbond_nbd_refined 0.279 r_symmetry_nbd_refined 0.263 r_nbd_refined 0.24 r_xyhbond_nbd_other 0.192 r_nbd_other 0.181 r_nbtor_refined 0.177 r_symmetry_nbd_other 0.173 r_symmetry_xyhbond_nbd_other 0.149 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.058 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1424 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing