ELECTRON MICROSCOPY

Sample

Clostridioides difficile Toxin B (TcdB) complexed with the synthetic bile acid methyl cholate

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument LEICA EM GP
Cryogen Name ETHANE
Sample Vitrification Details 30s preblot incubation on grid. 2-3s blot time.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 339310
Reported Resolution (Å) 2.87
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol OTHER
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Predicted models were docked into the map using ChimeraX. The model was then manually built with ISOLDE and Coot and refined with phenix.real_space_refine.
Data Acquisition
Detector Type FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å2) 40
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 2000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 75000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
IMAGE ACQUISITION EPU 3.7
MODEL FITTING ISOLDE ?
MODEL FITTING Coot 09.8.91
INITIAL EULER ASSIGNMENT cryoSPARC 4
FINAL EULER ASSIGNMENT cryoSPARC 4
CLASSIFICATION cryoSPARC 4
RECONSTRUCTION cryoSPARC 4
MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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