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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, 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 67.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.13 α = 90 b = 157.693 β = 90 c = 107.217 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 0.97856 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 2.55 78.85 96 0.997 14.2 12.3 36575
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 2.55 2.61 0.947
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 2.55 78.85 36501 1828 96.192 0.2 0.1975 0.2025 0.249 0.2504 31.426
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] 0.127 -0.086 -0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 20.336 r_dihedral_angle_3_deg 18.637 r_dihedral_angle_1_deg 7.624 r_lrange_it 7.499 r_lrange_other 7.497 r_scangle_it 5.053 r_scangle_other 5.034 r_mcangle_it 4.673 r_mcangle_other 4.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 20.336 r_dihedral_angle_3_deg 18.637 r_dihedral_angle_1_deg 7.624 r_lrange_it 7.499 r_lrange_other 7.497 r_scangle_it 5.053 r_scangle_other 5.034 r_mcangle_it 4.673 r_mcangle_other 4.673 r_scbond_it 3.172 r_scbond_other 3.139 r_mcbond_it 2.881 r_mcbond_other 2.881 r_angle_refined_deg 1.693 r_angle_other_deg 1.296 r_nbd_refined 0.207 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.166 r_nbd_other 0.162 r_metal_ion_refined 0.16 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.109 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.009 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 187 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing