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Crystal Structure of Treponema denticola Sialidase (TDE_0471)
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 7.4 296 25 mM Citric acid, 75 mM Bis-tris propane, pH 7.4, 20 mM Cadmium chloride, 25% PEG400, seeded
Crystal Properties Matthews coefficient Solvent content 3.18 61.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.794 α = 90 b = 65.479 β = 106.783 c = 92.042 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 1.627 45.71 95.8 0.109 0.985 5.7 2.7 88676 12.73
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 1.63 1.67 88.5 1.033 0.571 1 2.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.627 45.709 88640 4601 95.527 0.165 0.1638 0.1711 0.1869 0.1954 17.401
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] -1.579 -0.224 1.476 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.711 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_2_deg 7.924 r_dihedral_angle_1_deg 7.366 r_lrange_it 5.906 r_lrange_other 5.741 r_scangle_it 3.168 r_scangle_other 3.167 r_scbond_it 2.601 r_scbond_other 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.711 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_2_deg 7.924 r_dihedral_angle_1_deg 7.366 r_lrange_it 5.906 r_lrange_other 5.741 r_scangle_it 3.168 r_scangle_other 3.167 r_scbond_it 2.601 r_scbond_other 2.6 r_angle_refined_deg 1.601 r_mcangle_other 1.422 r_mcangle_it 1.416 r_mcbond_it 0.915 r_mcbond_other 0.915 r_angle_other_deg 0.561 r_metal_ion_refined 0.308 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.198 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.151 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.08 r_chiral_restr_other 0.018 r_bond_refined_d 0.013 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 3910 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement Coot model building BUCCANEER model building PHASER phasing Aimless data scaling xia2 data reduction DIALS data reduction