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X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated 24 h with [VIVO(acac)2]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.0 M MAGNESIUM CHLORIDE, 0.1 M bicine buffer pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.06 59.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.71 α = 90 b = 183.71 β = 90 c = 183.71 γ = 90
Symmetry Space Group F 4 3 2
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 PILATUS 6M 2024-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.498 92.024 93.4 0.2 0.999 20.9 68.1 40254
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 1.5 1.52 81.1 0.326 48.7
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 1.498 92.024 40089 2001 92.969 0.165 0.163 0.1727 0.1958 0.2009 24.824
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.289 r_dihedral_angle_4_deg 20.615 r_dihedral_angle_3_deg 13.942 r_lrange_it 9.697 r_lrange_other 9.419 r_dihedral_angle_1_deg 6.875 r_scangle_other 6.286 r_scangle_it 6.192 r_mcangle_it 4.283 r_mcangle_other 4.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.289 r_dihedral_angle_4_deg 20.615 r_dihedral_angle_3_deg 13.942 r_lrange_it 9.697 r_lrange_other 9.419 r_dihedral_angle_1_deg 6.875 r_scangle_other 6.286 r_scangle_it 6.192 r_mcangle_it 4.283 r_mcangle_other 4.275 r_scbond_it 4.25 r_scbond_other 4.014 r_mcbond_it 2.797 r_mcbond_other 2.789 r_angle_refined_deg 2.117 r_angle_other_deg 1.616 r_nbd_refined 0.254 r_metal_ion_refined 0.239 r_xyhbond_nbd_refined 0.226 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_other 0.181 r_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.173 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1424 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing