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X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure A)
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 2.05 40.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.55 α = 90 b = 80.55 β = 90 c = 36.28 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 PILATUS3 6M 2023-05-11 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) Rrim I (All) Rpim I (All) 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 1.45 56.96 99.8 0.085 0.088 0.024 0.999 16.8 14.2 21715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 100 1.199 1.241 0.318 0.831 14.8
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 1.45 56.957 21093 1057 97.042 0.197 0.1956 0.2043 0.2189 0.2305 16.855
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] -0.068 -0.068 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.863 r_dihedral_angle_3_deg 15.647 r_dihedral_angle_2_deg 11.978 r_dihedral_angle_1_deg 6.955 r_lrange_other 6.034 r_lrange_it 6.031 r_scangle_other 4.137 r_scangle_it 4.124 r_scbond_it 2.733 r_scbond_other 2.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.863 r_dihedral_angle_3_deg 15.647 r_dihedral_angle_2_deg 11.978 r_dihedral_angle_1_deg 6.955 r_lrange_other 6.034 r_lrange_it 6.031 r_scangle_other 4.137 r_scangle_it 4.124 r_scbond_it 2.733 r_scbond_other 2.644 r_mcangle_other 2.334 r_mcangle_it 2.33 r_angle_refined_deg 1.691 r_mcbond_it 1.558 r_mcbond_other 1.496 r_angle_other_deg 0.585 r_xyhbond_nbd_refined 0.375 r_symmetry_nbd_refined 0.309 r_nbd_refined 0.259 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.155 r_chiral_restr 0.086 r_nbd_other 0.086 r_symmetry_nbtor_other 0.081 r_symmetry_metal_ion_refined 0.064 r_metal_ion_refined 0.04 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing