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X-ray structure of lysozyme obtained upon reaction with the dioxidovanadium(V) complex with thiophene-2-carboxylic acid (3-ethoxy-2-hydroxybenzylidene)hydrazide
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 293 1.1 M sodium chloride, 0.1 M sodium acetate at pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.88 34.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.57 α = 90 b = 76.57 β = 90 c = 36.73 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 2024-06-04 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 1.31 38.29 91.1 0.999 13.3 22.4 24505
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 1.31 1.33 0.326
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 1.37 38.29 20294 1003 86.368 0.197 0.1951 0.202 0.233 0.2379 27.59
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] -0.099 -0.099 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.981 r_dihedral_angle_4_deg 27.219 r_dihedral_angle_3_deg 15.603 r_lrange_it 7.578 r_lrange_other 7.193 r_dihedral_angle_1_deg 6.626 r_scangle_it 5.093 r_scangle_other 5.06 r_mcangle_other 3.533 r_mcangle_it 3.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.981 r_dihedral_angle_4_deg 27.219 r_dihedral_angle_3_deg 15.603 r_lrange_it 7.578 r_lrange_other 7.193 r_dihedral_angle_1_deg 6.626 r_scangle_it 5.093 r_scangle_other 5.06 r_mcangle_other 3.533 r_mcangle_it 3.513 r_scbond_it 3.303 r_scbond_other 3.217 r_mcbond_it 2.461 r_mcbond_other 2.412 r_angle_refined_deg 1.817 r_angle_other_deg 1.569 r_nbd_refined 0.236 r_nbd_other 0.224 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.188 r_xyhbond_nbd_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.185 r_metal_ion_refined 0.174 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 81 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing