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Crystal Structure of Treponema denticola Sialidase (TDE_0471) D165A mutant bound to 3'-sialyllactose (only Neu5Ac visible)
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 6.5 296 100 mM Bis-tris, pH 6.5, 20 mM Cadmium chliride, 23% PEG400, 5 mM 3'-sialyllactose
Crystal Properties Matthews coefficient Solvent content 3.27 62.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.445 α = 90 b = 66.077 β = 106.62 c = 93.115 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 PILATUS 6M 2023-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0331 APS 23-ID-D
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 1.81 46.172 99.7 0.174 0.979 4.8 2.9 69062 11.5
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 1.81 1.86 99.5 1.108 0.429 1.2 2.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.81 46.172 69036 3493 99.554 0.166 0.1649 0.1898 0.1941 16.484
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] -0.957 -0.464 1.227 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.452 r_dihedral_angle_3_deg 12.968 r_dihedral_angle_2_deg 8.716 r_dihedral_angle_1_deg 7.841 r_lrange_it 5.461 r_lrange_other 5.196 r_scangle_it 2.836 r_scangle_other 2.835 r_scbond_it 2.153 r_scbond_other 2.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.452 r_dihedral_angle_3_deg 12.968 r_dihedral_angle_2_deg 8.716 r_dihedral_angle_1_deg 7.841 r_lrange_it 5.461 r_lrange_other 5.196 r_scangle_it 2.836 r_scangle_other 2.835 r_scbond_it 2.153 r_scbond_other 2.152 r_angle_refined_deg 1.863 r_mcangle_it 1.597 r_mcangle_other 1.597 r_mcbond_it 1.005 r_mcbond_other 1.005 r_angle_other_deg 0.627 r_metal_ion_refined 0.502 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.198 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.155 r_nbd_other 0.122 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.087 r_symmetry_metal_ion_refined 0.043 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.014 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 3889 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Coot model building BUCCANEER model building PHASER phasing Aimless data scaling xia2 data reduction DIALS data reduction