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Crystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only (treated with DMSO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 67.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.1 α = 90 b = 156.777 β = 90 c = 107.11 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 2025-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97946 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.52 74.32 90.4 0.992 9.1 11.5 26235
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 2.52 2.77 0.596
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 2.52 74.32 26235 1324 66.34 0.181 0.1767 0.1821 0.2598 0.2578 40.236
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] -0.377 0.124 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_4_deg 20.327 r_dihedral_angle_3_deg 19.266 r_lrange_it 9.232 r_lrange_other 9.217 r_dihedral_angle_1_deg 7.862 r_scangle_it 6.403 r_scangle_other 6.395 r_mcangle_it 5.582 r_mcangle_other 5.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_4_deg 20.327 r_dihedral_angle_3_deg 19.266 r_lrange_it 9.232 r_lrange_other 9.217 r_dihedral_angle_1_deg 7.862 r_scangle_it 6.403 r_scangle_other 6.395 r_mcangle_it 5.582 r_mcangle_other 5.581 r_scbond_it 3.877 r_scbond_other 3.858 r_mcbond_it 3.469 r_mcbond_other 3.454 r_angle_refined_deg 1.645 r_angle_other_deg 1.305 r_nbd_refined 0.21 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.167 r_nbd_other 0.136 r_symmetry_xyhbond_nbd_refined 0.116 r_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.071 r_symmetry_nbd_refined 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5045 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing