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X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein is treated 6 days 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 293 0.1 M bicine buffer pH 9.0, 2.0 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.28 α = 90 b = 183.28 β = 90 c = 183.28 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 1.54 91.808 95.6 0.169 1 22.7 66.6 37529
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 1.54 1.57 100 0.359 0.5 59.3
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 1.543 91.808 36982 1859 94.193 0.177 0.1762 0.1859 0.1979 0.2051 31.166
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 39.116 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 13.319 r_lrange_it 8.915 r_lrange_other 8.528 r_scangle_other 6.552 r_scangle_it 6.505 r_dihedral_angle_1_deg 5.502 r_scbond_it 4.702 r_scbond_other 4.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.116 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 13.319 r_lrange_it 8.915 r_lrange_other 8.528 r_scangle_other 6.552 r_scangle_it 6.505 r_dihedral_angle_1_deg 5.502 r_scbond_it 4.702 r_scbond_other 4.485 r_mcangle_it 4.102 r_mcangle_other 4.101 r_mcbond_other 2.812 r_mcbond_it 2.81 r_angle_refined_deg 2.066 r_angle_other_deg 1.531 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.233 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbd_refined 0.179 r_metal_ion_refined 0.177 r_nbtor_refined 0.172 r_symmetry_nbd_other 0.171 r_nbd_other 0.15 r_symmetry_xyhbond_nbd_other 0.119 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.081 r_symmetry_metal_ion_refined 0.039 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1424 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing