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Crystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only
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 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.154 α = 90 b = 158.028 β = 90 c = 107.621 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 EIGER2 S 16M 2025-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.99987 MAX IV BioMAX
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 2.16 104.01 92.8 0.985 6.2 8 47443
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 2.16 2.35 0.263
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 2.16 104.01 47442 2373 74.613 0.187 0.1846 0.1911 0.2321 0.2343 38.431
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] -0.583 0.433 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 20.09 r_dihedral_angle_3_deg 18.056 r_lrange_it 9.004 r_lrange_other 9 r_dihedral_angle_1_deg 7.348 r_scangle_it 6.476 r_scangle_other 6.475 r_mcangle_it 5.233 r_mcangle_other 5.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 20.09 r_dihedral_angle_3_deg 18.056 r_lrange_it 9.004 r_lrange_other 9 r_dihedral_angle_1_deg 7.348 r_scangle_it 6.476 r_scangle_other 6.475 r_mcangle_it 5.233 r_mcangle_other 5.233 r_scbond_it 4.127 r_scbond_other 4.103 r_mcbond_it 3.378 r_mcbond_other 3.377 r_angle_refined_deg 1.63 r_angle_other_deg 1.321 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.168 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.144 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5201 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing