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Crystal structure of SusG 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 experimental model PDB 6BS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M Carboxylic acids (Na-Formate; NH 4-Acetate; Na 3 -Citrate; NaK-Tartrate (racemic); Na-Oxamate), 0.1 M Buffer System 1 (Imidazole; MES (acid)) pH 6.5, 50 % v/v Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.293 α = 90 b = 127.293 β = 90 c = 129.184 γ = 90
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) 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 2.65 64.59 100 0.995 5.8 14.1 59811
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 2.65 2.72 0.418
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 2.65 63.65 56734 3006 99.87 0.20887 0.20577 0.2104 0.26945 0.2672 RANDOM 73.834
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] -3.76 -3.76 7.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.854 r_long_range_B_refined 13.291 r_long_range_B_other 13.29 r_mcangle_it 10.513 r_mcangle_other 10.512 r_scangle_other 10.255 r_mcbond_it 7.155 r_dihedral_angle_1_deg 7.146 r_mcbond_other 7.137 r_dihedral_angle_2_deg 7.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.854 r_long_range_B_refined 13.291 r_long_range_B_other 13.29 r_mcangle_it 10.513 r_mcangle_other 10.512 r_scangle_other 10.255 r_mcbond_it 7.155 r_dihedral_angle_1_deg 7.146 r_mcbond_other 7.137 r_dihedral_angle_2_deg 7.029 r_scbond_it 6.938 r_scbond_other 6.917 r_angle_refined_deg 1.524 r_angle_other_deg 0.568 r_chiral_restr 0.217 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 10067 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing