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X-ray structure of lysozyme obtained upon reaction with the dioxidovanadium(V) complex with furan-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 4 293 1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.9 35.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.846 α = 90 b = 76.846 β = 90 c = 36.839 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 EIGER2 S 16M 2023-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.24 54.34 100 0.999 15 20 32110
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 1.24 1.26 0.412
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 1.24 54.338 31754 1554 99.689 0.205 0.203 0.2129 0.2559 0.2642 24.679
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] 0.095 0.095 -0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.222 r_dihedral_angle_4_deg 19.309 r_dihedral_angle_3_deg 14.953 r_dihedral_angle_1_deg 6.696 r_lrange_it 5.677 r_lrange_other 5.446 r_scangle_it 4.295 r_scangle_other 4.191 r_mcangle_it 2.96 r_mcangle_other 2.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.222 r_dihedral_angle_4_deg 19.309 r_dihedral_angle_3_deg 14.953 r_dihedral_angle_1_deg 6.696 r_lrange_it 5.677 r_lrange_other 5.446 r_scangle_it 4.295 r_scangle_other 4.191 r_mcangle_it 2.96 r_mcangle_other 2.958 r_scbond_it 2.728 r_scbond_other 2.638 r_mcbond_it 2.159 r_mcbond_other 2.157 r_angle_refined_deg 1.86 r_angle_other_deg 1.541 r_nbd_refined 0.25 r_symmetry_xyhbond_nbd_refined 0.249 r_xyhbond_nbd_refined 0.235 r_nbd_other 0.221 r_symmetry_nbd_refined 0.213 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.18 r_metal_ion_refined 0.131 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 106 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing