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X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2</sub>] at 310 K
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 4 310 1,1 M sodium chloride and 0,1 M sodium acetate buffer pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.86 α = 90 b = 80.86 β = 90 c = 36.83 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 310 PIXEL DECTRIS PILATUS 6M 2024-11-20 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 1.83 57.177 90 0.116 0.997 8.9 8.7 10096
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 100 6.402 0.369 0.3 8.8
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 1.831 57.177 8732 428 77.721 0.205 0.2001 0.207 0.2838 0.292 40.129
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] -0.389 -0.389 0.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.956 r_dihedral_angle_3_deg 15.382 r_lrange_it 9.008 r_lrange_other 8.892 r_dihedral_angle_2_deg 8.367 r_dihedral_angle_1_deg 7.519 r_scangle_other 5.848 r_scangle_it 5.651 r_scbond_it 4.563 r_mcangle_other 4.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.956 r_dihedral_angle_3_deg 15.382 r_lrange_it 9.008 r_lrange_other 8.892 r_dihedral_angle_2_deg 8.367 r_dihedral_angle_1_deg 7.519 r_scangle_other 5.848 r_scangle_it 5.651 r_scbond_it 4.563 r_mcangle_other 4.092 r_mcangle_it 4.091 r_scbond_other 3.955 r_mcbond_it 3.159 r_mcbond_other 3.118 r_angle_refined_deg 1.847 r_angle_other_deg 0.469 r_xyhbond_nbd_refined 0.425 r_symmetry_nbd_refined 0.312 r_symmetry_metal_ion_refined 0.285 r_nbd_refined 0.267 r_nbd_other 0.212 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_refined 0.209 r_nbtor_refined 0.181 r_metal_ion_refined 0.09 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing