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Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to octadecavanadate ion (structure B)
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 4 298 20% ethylene glycol,
0.1 M sodium acetate buffer pH 4.0,
0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.39 α = 90 b = 80.39 β = 90 c = 36.51 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 2021-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 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 1.79 40.19 99.8 0.104 1 33.6 20 11611
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 1.79 1.83 100 1.06 0.912 4.6 15
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 THROUGHOUT 1.797 40.128 11398 580 97.938 0.183 0.1805 0.1875 0.2325 0.2474 26.962
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] -0.219 -0.219 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_3_deg 15.367 r_lrange_it 7.157 r_dihedral_angle_1_deg 6.864 r_lrange_other 6.786 r_scangle_other 4.817 r_scangle_it 4.651 r_mcangle_other 3.243 r_mcangle_it 3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_3_deg 15.367 r_lrange_it 7.157 r_dihedral_angle_1_deg 6.864 r_lrange_other 6.786 r_scangle_other 4.817 r_scangle_it 4.651 r_mcangle_other 3.243 r_mcangle_it 3.23 r_scbond_other 2.995 r_scbond_it 2.974 r_mcbond_it 2.29 r_mcbond_other 2.253 r_angle_refined_deg 2.071 r_angle_other_deg 1.415 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.241 r_metal_ion_refined 0.232 r_xyhbond_nbd_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_other 0.188 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.161 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.081 r_symmetry_metal_ion_refined 0.048 r_xyhbond_nbd_other 0.047 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing