ELECTRON MICROSCOPY

Sample

Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details 2 minute incubation time; blot time of 6-7.5 seconds; and blot offset of -2 mm
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 10581
Reported Resolution (Å) 9.83
Resolution Method FSC 0.143 CUT-OFF
Other Details emClarity: The two half-dataset volumes were combined with a B-170 factor of 0, and the Gold standard FSC at 0.143 was calculated to be 9.83 A with anisotropic resolutions ranging from 8.89-16.17 Angstrom.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space RECIPROCAL
Refinement Protocol RIGID BODY FIT
Refinement Target Correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Eliminate minor clashes between FlaB1, FcpA, and FcpB
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 1.7
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI POLARA 300
Minimum Defocus (nm) 3000
Maximum Defocus (nm) 5000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model SIDE ENTRY, EUCENTRIC
Nominal Magnification 15000
Calibrated Magnification 19230
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
VOLUME SELECTION PEET 1.11
VOLUME SELECTION RELION 2.1
IMAGE ACQUISITION SerialEM 3
CTF CORRECTION IMOD 4.9.4_RHEL6-64_CUDA8.0
CTF CORRECTION RELION 2.1.b1-gcccuda-2016.10-cc37
CTF CORRECTION emClarity 1..0
MODEL FITTING Rosetta 3
MODEL FITTING Situs 2.8-foss-2016b
MODEL FITTING UCSF Chimera 1.12
FINAL EULER ASSIGNMENT RELION 2.1.b1-gcccuda-2016.10-cc37
FINAL EULER ASSIGNMENT emClarity 1.0
RECONSTRUCTION emClarity 1.1
MODEL REFINEMENT Rosetta 3
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF estimation was initially done in IMOD.