ELECTRON MICROSCOPY

Sample

Toxin B in complex with scFv 6

Specimen Preperation
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 19969
Reported Resolution (Å) 3.60
Resolution Method FSC 0.143 CUT-OFF
Other Details Non Uniform Refinement
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details TcdB was built using the published 3.87 Angstrom crystal structure as a starting model (PDB: 6OQ5). The three bound VHH domains in the crystal structure were removed in PyMOL, and the structure was docked into density using Chimera. The initial model was refined in Coot before alignment with the design model in PyMOL, the scFv docked well in density. The entire model was refined with iterative rounds in Coot, Interactive Structure Optimization by Local Direct Exploration (ISOLDE) were performed at a simulated 25 Kelvin, and Phenix real-space refinement. The final model quality was analyzed using Molprobity.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 44
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS GLACIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1800
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 45000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF
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