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Crystal Structure of Treponema denticola Sialidase (TDE_0471) Bound to Neu5Ac (NANA)
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 8.2 296 100 mM Tris, pH 8.2, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 15 mM Neu5Ac
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.734 α = 90 b = 65.371 β = 106.19 c = 92.021 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 1.56 57.95 97.3 0.075 0.997 11.2 4.6 102901 12.28
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 1.56 1.6 90.2 0.422 0.912 3 4.4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.56 57.95 97730 5155 97.25 0.14267 0.14184 0.15848 0.1792 RANDOM 21.4
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] -1.6 -0.24 0.46 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.78 r_dihedral_angle_2_deg 8.759 r_dihedral_angle_1_deg 7.607 r_long_range_B_refined 5.466 r_long_range_B_other 5.257 r_scangle_other 3.115 r_scbond_it 3.095 r_scbond_other 3.095 r_angle_refined_deg 1.689 r_mcangle_other 1.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.78 r_dihedral_angle_2_deg 8.759 r_dihedral_angle_1_deg 7.607 r_long_range_B_refined 5.466 r_long_range_B_other 5.257 r_scangle_other 3.115 r_scbond_it 3.095 r_scbond_other 3.095 r_angle_refined_deg 1.689 r_mcangle_other 1.689 r_mcangle_it 1.688 r_mcbond_it 1.127 r_mcbond_other 1.127 r_angle_other_deg 0.578 r_chiral_restr 0.086 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3915 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement Coot model building BUCCANEER model building PHASER phasing Aimless data scaling xia2 data reduction DIALS data reduction