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The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.01M RbCl, 0.01M SrAc2, 0.01M CsAc, 0.01M BaAc2, 0.1M BES, TEA pH7.5, 12.5% PEG4,000, 20% 1,2,6- Hexanetriol
Crystal Properties Matthews coefficient Solvent content 5.36 77.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.166 α = 90 b = 268.755 β = 90 c = 194.862 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 6M 2022-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95370 CLSI 08ID-1
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 3.95 49.15 99.9 0.998 10.2 8.9 36051
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 3.95 4.13 0.743
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 3.95 49.15 36024 1789 99.917 0.247 0.244 0.2409 0.3002 0.2954 147.016
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] 2.927 -0.656 -2.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.762 r_lrange_it 11.475 r_lrange_other 11.475 r_dihedral_angle_6_deg 9.106 r_mcangle_it 7.592 r_mcangle_other 7.592 r_scangle_it 7.409 r_scangle_other 7.409 r_dihedral_angle_1_deg 5.76 r_mcbond_it 4.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.762 r_lrange_it 11.475 r_lrange_other 11.475 r_dihedral_angle_6_deg 9.106 r_mcangle_it 7.592 r_mcangle_other 7.592 r_scangle_it 7.409 r_scangle_other 7.409 r_dihedral_angle_1_deg 5.76 r_mcbond_it 4.413 r_mcbond_other 4.411 r_scbond_it 4.36 r_scbond_other 4.346 r_dihedral_angle_2_deg 3.079 r_angle_refined_deg 0.801 r_angle_other_deg 0.319 r_nbd_refined 0.2 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.17 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.076 r_symmetry_nbtor_other 0.069 r_nbd_other 0.062 r_ncsr_local_group_1 0.052 r_symmetry_nbd_refined 0.05 r_ncsr_local_group_2 0.048 r_ncsr_local_group_3 0.047 r_chiral_restr 0.039 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13251 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing