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Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UWR
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.154 f_angle_d 0.458 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Sample Single heptamer (class 1) of Clostridioides difficile binary toxin translocase CDTb wild-type after depletion of calcium from RBD1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 33531 Reported Resolution (Å) 3.06 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C7
Map-Model Fitting and Refinement Id Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details 1 (6UWR) AB INITIO MODEL 2 (6UWR) AB INITIO MODEL 3 (6UWR) AB INITIO MODEL 4 (6UWR) AB INITIO MODEL 5 (6UWR) AB INITIO MODEL 6 (6UWR) AB INITIO MODEL 7 (6UWR) AB INITIO MODEL
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 45000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.2 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.3.2 MODEL FITTING UCSF Chimera MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC 3.3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.3.2 CLASSIFICATION cryoSPARC 3.3.2 RECONSTRUCTION cryoSPARC 3.3.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1109860