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Crystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q73QH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 296 100 mM HEPES, pH 7.8, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 25 mM DANA for 20 min
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.811 α = 90 b = 65.547 β = 106.148 c = 91.679 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2022-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0331 APS 23-ID-B
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 1.549 59.314 97.1 0.077 0.994 11.8 4.7 104014 9.5
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 1.55 1.59 94.6 0.274 0.943 4.5 4.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.549 59.314 104006 5239 96.852 0.139 0.1378 0.1505 0.153 0.1636 Random 14.886
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] -1.307 -0.15 0.854 0.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.096 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_2_deg 7.71 r_dihedral_angle_1_deg 7.588 r_lrange_it 4.657 r_lrange_other 4.424 r_scangle_it 2.526 r_scangle_other 2.526 r_scbond_it 2.094 r_scbond_other 2.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.096 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_2_deg 7.71 r_dihedral_angle_1_deg 7.588 r_lrange_it 4.657 r_lrange_other 4.424 r_scangle_it 2.526 r_scangle_other 2.526 r_scbond_it 2.094 r_scbond_other 2.093 r_dihedral_angle_other_3_deg 2.029 r_angle_refined_deg 1.656 r_mcangle_it 1.383 r_mcangle_other 1.383 r_mcbond_it 0.933 r_mcbond_other 0.923 r_angle_other_deg 0.579 r_symmetry_nbd_refined 0.364 r_nbd_other 0.274 r_nbd_refined 0.205 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.18 r_metal_ion_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.151 r_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.086 r_symmetry_metal_ion_refined 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3918 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement Coot model building BUCCANEER model building PHASER phasing Aimless data scaling xia2 data reduction DIALS data reduction