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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, SITTING 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 = 137.098 α = 90 b = 156.774 β = 90 c = 107.108 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 3.2 74.32 93.7 0.995 12.4 10.6 18284
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 3.2 3.25 0.921
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 3.2 74.32 18209 914 93.75 0.183 0.1797 0.1827 0.2491 0.2489 44.185
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] 0.03 -0.04 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.28 r_dihedral_angle_4_deg 19.585 r_dihedral_angle_3_deg 19.579 r_dihedral_angle_1_deg 8.132 r_lrange_it 7.994 r_lrange_other 7.994 r_scangle_other 5.325 r_scangle_it 5.323 r_mcangle_it 5.199 r_mcangle_other 5.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.28 r_dihedral_angle_4_deg 19.585 r_dihedral_angle_3_deg 19.579 r_dihedral_angle_1_deg 8.132 r_lrange_it 7.994 r_lrange_other 7.994 r_scangle_other 5.325 r_scangle_it 5.323 r_mcangle_it 5.199 r_mcangle_other 5.199 r_scbond_it 3.199 r_scbond_other 3.198 r_mcbond_it 3.172 r_mcbond_other 3.172 r_angle_refined_deg 1.567 r_angle_other_deg 1.247 r_nbd_refined 0.215 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.153 r_xyhbond_nbd_refined 0.144 r_nbd_other 0.142 r_metal_ion_refined 0.138 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.055 r_symmetry_xyhbond_nbd_refined 0.041 r_bond_refined_d 0.007 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 5138 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing