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Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 200 mM Ammonium phosphate monobasic, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.5 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.087 α = 90 b = 121.34 β = 90 c = 206.417 γ = 90
Symmetry Space Group P 21 21 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 CCD RAYONIX MX225HE 2019-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.82 121.34 99.8 0.07 0.99 13.8 7.3 115828
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 1.82 1.85 97.8 1.6 0.62 1 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5UQM 1.82 104.61 109893 5826 99.75 0.2172 0.2154 0.2256 0.2515 0.2593 RANDOM 43.184
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] 2.84 1.26 -4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 21.764 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 6.466 r_angle_refined_deg 1.412 r_angle_other_deg 1.315 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 21.764 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 6.466 r_angle_refined_deg 1.412 r_angle_other_deg 1.315 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8851 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing