ELECTRON MICROSCOPY

Sample

Csu pilus rod type 2 stack

Specimen Preperation
Sample Aggregation State 2D ARRAY
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 687088
Reported Resolution (Å) 4.70
Resolution Method FSC 0.143 CUT-OFF
Other Details Local Refinement allowed generating a single map without individual particles flipping and settling into pseudosymmetric orientations.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value 330.69
Fitting Procedure ?
Details UCSF Chimera was used to first fit the subunits into the single native pilus rod map (PDB Accession ID: 9I37) and average their relative angles, and it was also used to adjust pixel spacing of all maps to match model dimensions. Coot was used to adjust side chain and loop positions. A pair of antiparallel pili with subunit angles adjusted to 3-turns-per-7-subunits symmetry was overlapped with a 2D class to adjust the binding junction angle. Finally, Phenix was used to fit the type 2 stack model into the map.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 59.848
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 400
Maximum Defocus (nm) 1600
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 105000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC v4.5.3
IMAGE ACQUISITION EPU v3.60
CTF CORRECTION cryoSPARC v4.5.3
MODEL FITTING UCSF Chimera 1.15
MODEL FITTING Coot 0.8.9.2 EL
MODEL REFINEMENT PHENIX 1.20.1_4487:
INITIAL EULER ASSIGNMENT cryoSPARC v4.5.3
FINAL EULER ASSIGNMENT cryoSPARC v4.5.3
CLASSIFICATION cryoSPARC v4.5.3
RECONSTRUCTION cryoSPARC v4.5.3
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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