☰ Navigation Tabs
Crystal structure of the adduct formed upon reaction of [V(IV)O(acetylacetonate)2] with 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 3.82 67.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.133 α = 90 b = 157.695 β = 90 c = 107.218 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 1.93 78.85 95 0.998 11.2 12.3 47778
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 1.93 2.17 0.788
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 1.93 78.85 47778 2337 54.845 0.188 0.1858 0.1928 0.2349 0.2371 37.377
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] 0.105 -0.235 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.028 r_dihedral_angle_4_deg 21.415 r_dihedral_angle_3_deg 18.153 r_lrange_it 8.01 r_lrange_other 7.929 r_dihedral_angle_1_deg 7.278 r_scangle_it 5.507 r_scangle_other 5.486 r_mcangle_it 4.565 r_mcangle_other 4.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.028 r_dihedral_angle_4_deg 21.415 r_dihedral_angle_3_deg 18.153 r_lrange_it 8.01 r_lrange_other 7.929 r_dihedral_angle_1_deg 7.278 r_scangle_it 5.507 r_scangle_other 5.486 r_mcangle_it 4.565 r_mcangle_other 4.564 r_scbond_it 3.513 r_scbond_other 3.49 r_mcbond_it 2.96 r_mcbond_other 2.954 r_angle_refined_deg 1.766 r_angle_other_deg 1.286 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_refined 0.195 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.165 r_metal_ion_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.156 r_nbd_other 0.124 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_other 0.08 r_symmetry_xyhbond_nbd_other 0.079 r_chiral_restr 0.074 r_bond_refined_d 0.008 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 472 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing