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X-ray structure of decavanadate/lysozyme adduct obtained when the protein is treated with Cs2[V(V)2O4(mal)2]2H2O (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 4 293 1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.03 39.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.01 α = 90 b = 80.01 β = 90 c = 36.27 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 2024-10-14 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) 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 1.18 40.01 89.1 0.999 19.4 20 35010
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 1.18 1.2 0.371
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 1.18 40.01 28531 1341 72.622 0.193 0.1914 0.2 0.2347 0.2396 25.367
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] -0.564 -0.564 1.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.245 r_dihedral_angle_4_deg 22.207 r_dihedral_angle_3_deg 14.271 r_scangle_it 7.236 r_dihedral_angle_1_deg 7.197 r_lrange_it 6.124 r_scangle_other 6.107 r_scbond_it 5.811 r_lrange_other 5.489 r_rigid_bond_restr 5.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.245 r_dihedral_angle_4_deg 22.207 r_dihedral_angle_3_deg 14.271 r_scangle_it 7.236 r_dihedral_angle_1_deg 7.197 r_lrange_it 6.124 r_scangle_other 6.107 r_scbond_it 5.811 r_lrange_other 5.489 r_rigid_bond_restr 5.264 r_scbond_other 5.003 r_mcangle_other 4.14 r_mcangle_it 4.139 r_mcbond_it 3.499 r_mcbond_other 3.48 r_angle_refined_deg 2.414 r_angle_other_deg 1.642 r_symmetry_nbd_refined 0.29 r_nbd_refined 0.249 r_symmetry_nbd_other 0.2 r_xyhbond_nbd_refined 0.18 r_nbd_other 0.174 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.16 r_chiral_restr 0.103 r_metal_ion_refined 0.085 r_symmetry_nbtor_other 0.084 r_symmetry_metal_ion_refined 0.044 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing