ELECTRON MICROSCOPY

Sample

Conjugative pilus from the E. coli R388 plasmid

Specimen Preperation
Sample Aggregation State HELICAL ARRAY
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details C-flat grids (Protochips, US 1.2/1.3 400 mesh) were negatively glow discharged using PELCO Easiglow (Ted Pella, USA) and coated with graphene oxide. 3 microliter of the purified pili sample was applied on each grid and a Vitrobot Mark IV (Thermo Fisher Scientific, USA) operating at 4C and 100 percent humidity was used to incubate the sample on the grid for 30 secs and blotting for 16 secs (blot force -10) prior to vitrification in liquid ethane.
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 209930
Reported Resolution (Å) 3.39
Resolution Method FSC 0.143 CUT-OFF
Other Details Find more details in the Methods section of the publication
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol RIGID BODY FIT
Refinement Target Cross-correlation in Phenix
Overall B Value 109.7
Fitting Procedure ?
Details Find more details in the Methods section of the publication
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 34.67
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 900
Maximum Defocus (nm) 2400
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 81000
Calibrated Magnification 81000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details The R388 pilus data were collected at the ISMB Birkbeck EM facility using a Titan Krios microscope (Thermo Fisher Scientific, USA) operated at 300 keV and equipped with a BioQuantum energy filter (Gatan, USA) with a slit width of 20 eV. The images were collected with a post-GIF K3 direct electron detector (Gatan, USA) operating in super resolution mode, at a magnification of 81,000 corresponding to a pixel size of 1.067 A. The dose rate was set to 14.62 e per pixel per second and a total dose of 34.67 e per A2 was fractionated over 50 frames.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC CRYOSPARC v4.3.1
IMAGE ACQUISITION EPU ?
CTF CORRECTION cryoSPARC CRYOSPARC v4.3.1
MODEL FITTING Coot COOT v0.9.3
INITIAL EULER ASSIGNMENT cryoSPARC CRYOSPARC v4.3.1
FINAL EULER ASSIGNMENT cryoSPARC CRYOSPARC v4.3.1
CLASSIFICATION cryoSPARC CRYOSPARC v4.3.1
RECONSTRUCTION cryoSPARC CRYOSPARC v4.3.1
MODEL REFINEMENT PHENIX 1.21rc1_5058
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION Find more details in the Methods section of the publication