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X-ray structure of the adduct between human serum transferrin with Fe3+ bound at the C-lobe and diruthenium tetraacetate chloride
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 3.82 67.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.936 α = 90 b = 156.712 β = 90 c = 107.145 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 16M 2023-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 2.262 103.116 93.9 0.208 0.997 9.8 12.6 30700
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.262 2.502 0.734
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 2.262 103.116 30700 1528 56.823 0.182 0.1791 0.1853 0.2344 0.2375 44.34
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] -0.458 -0.335 0.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.681 r_dihedral_angle_6_deg 13.802 r_lrange_it 10.186 r_lrange_other 10.166 r_dihedral_angle_2_deg 9.091 r_dihedral_angle_1_deg 7.569 r_scangle_it 7.207 r_scangle_other 7.206 r_mcangle_it 6.109 r_mcangle_other 6.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.681 r_dihedral_angle_6_deg 13.802 r_lrange_it 10.186 r_lrange_other 10.166 r_dihedral_angle_2_deg 9.091 r_dihedral_angle_1_deg 7.569 r_scangle_it 7.207 r_scangle_other 7.206 r_mcangle_it 6.109 r_mcangle_other 6.108 r_scbond_it 4.286 r_scbond_other 4.285 r_mcbond_it 3.764 r_mcbond_other 3.761 r_angle_refined_deg 1.487 r_angle_other_deg 0.528 r_nbd_refined 0.222 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.175 r_nbd_other 0.132 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbd_refined 0.106 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.069 r_metal_ion_refined 0.059 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5201 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing