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X-ray structure of the adduct between human serum transferrin with Fe3+ bound at the C-lobe and dirhodium tetraacetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9THR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 15% (w/v) PEG 3350
16% (v/v) glycerol
8 mM disodium malonate
150 mM Na-PIPES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.87 68.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.776 α = 90 b = 157.085 β = 90 c = 107.559 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 9M 2025-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.368 103.58 92.8 0.205 0.996 10.3 13.4 33787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.368 2.604 58.1 2.088 0.581 1.5 11.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.37 103.58 33785 1724 70.905 0.186 0.1829 0.1882 0.2443 0.2493 44.057
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] -0.436 -0.013 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.741 r_dihedral_angle_2_deg 13.5 r_dihedral_angle_6_deg 13.325 r_lrange_other 10.241 r_lrange_it 10.229 r_scangle_it 8.267 r_scangle_other 8.165 r_dihedral_angle_1_deg 7.481 r_mcangle_it 6.481 r_mcangle_other 6.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.741 r_dihedral_angle_2_deg 13.5 r_dihedral_angle_6_deg 13.325 r_lrange_other 10.241 r_lrange_it 10.229 r_scangle_it 8.267 r_scangle_other 8.165 r_dihedral_angle_1_deg 7.481 r_mcangle_it 6.481 r_mcangle_other 6.48 r_scbond_it 5.035 r_scbond_other 4.898 r_mcbond_it 4.102 r_mcbond_other 4.096 r_angle_refined_deg 1.781 r_angle_other_deg 0.583 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.178 r_symmetry_nbd_refined 0.134 r_nbd_other 0.12 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.08 r_metal_ion_refined 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5201 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing