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X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2</sub>] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.33 α = 90 b = 78.33 β = 90 c = 37.05 γ = 90
Symmetry Space Group P 43 21 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 2023-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 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 1.17 55.39 99.1 0.143 0.996 15.3 23.1 41982
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.19 99.9 1.204 0.796 2.4 16.1
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 1.172 55.388 38859 1923 99.016 0.157 0.1557 0.1706 0.1891 0.1962 15.88
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] 0.092 0.092 -0.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.486 r_dihedral_angle_3_deg 12.45 r_dihedral_angle_2_deg 7.833 r_dihedral_angle_1_deg 6.814 r_rigid_bond_restr 5.104 r_lrange_it 3.731 r_scangle_it 3.668 r_lrange_other 3.493 r_scangle_other 3.263 r_scbond_it 3.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.486 r_dihedral_angle_3_deg 12.45 r_dihedral_angle_2_deg 7.833 r_dihedral_angle_1_deg 6.814 r_rigid_bond_restr 5.104 r_lrange_it 3.731 r_scangle_it 3.668 r_lrange_other 3.493 r_scangle_other 3.263 r_scbond_it 3.252 r_scbond_other 2.877 r_angle_refined_deg 2.286 r_mcangle_it 1.909 r_mcangle_other 1.909 r_mcbond_it 1.612 r_mcbond_other 1.6 r_angle_other_deg 0.644 r_nbd_refined 0.279 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.206 r_symmetry_xyhbond_nbd_other 0.206 r_symmetry_nbd_other 0.203 r_metal_ion_refined 0.184 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.18 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing