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Crystal structure of SusA amylase from Bacteroides thetaiotaomicron covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q8A1G0-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 50 mM MES pH 6.5, 50 mM imidazole, 20% (v/v) glycerol and 10% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.978 α = 90 b = 105.978 β = 90 c = 753.691 γ = 120
Symmetry Space Group P 32 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 EIGER2 XE 16M 2023-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.43 58.25 100 0.18 0.04 1 12 21.4 212465
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 2.43 2.49 0.32
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.43 58.25 178136 9306 99.95 0.23246 0.2299 0.2302 0.28148 0.2779 RANDOM 72.021
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] 0.02 0.01 0.02 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.307 r_long_range_B_refined 13.154 r_long_range_B_other 13.153 r_scangle_other 10.799 r_mcangle_it 10.544 r_mcangle_other 10.544 r_dihedral_angle_2_deg 9.924 r_scbond_it 7.553 r_scbond_other 7.552 r_mcbond_it 7.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.307 r_long_range_B_refined 13.154 r_long_range_B_other 13.153 r_scangle_other 10.799 r_mcangle_it 10.544 r_mcangle_other 10.544 r_dihedral_angle_2_deg 9.924 r_scbond_it 7.553 r_scbond_other 7.552 r_mcbond_it 7.498 r_mcbond_other 7.498 r_dihedral_angle_1_deg 6.851 r_angle_refined_deg 1.445 r_angle_other_deg 0.542 r_chiral_restr 0.235 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 27802 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 291
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing