ELECTRON MICROSCOPY

Sample

Rous sarcoma virus - Prague C

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details 2.5 seconds blotting time
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 40962
Reported Resolution (Å) 4.3
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 AB INITIO MODEL
Refinement Target Correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Three copies of CA monomer were rigid body-fitted into the EM density to accommodate the 3 symmetry independent CA copies. The fit was further refined in Coot. The symmetry independent copies were expanded according to the C2 symmetry, and an additional ring of CTDs adjacent to the CA hexamer was added to account for the continuous lattice during the refinement. The model was refined by iterating between automatic real space refinement in Phenix and manual model inspection/editing in Coot.
Data Acquisition
Detector Type GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å2) 3.5
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 4000
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 Areas of interest for high-resolution data collection were identified in low magnification montages. Prior to tomogram acquisition, gain references were acquired and the filter was fully tuned. Microscope tuning was performed using the FEI AutoCTF software. The ilumination mode used during acquisition was nanoprobe.
Imaging Experiment
Task Software Package Version
VOLUME SELECTION MATLAB R2018b
VOLUME SELECTION IMOD 4.9
VOLUME SELECTION Dynamo 1.1.333
IMAGE ACQUISITION SerialEM ?
IMAGE ACQUISITION DigitalMicrograph ?
CTF CORRECTION CTFFIND 4.1.10
CTF CORRECTION IMOD 4.9
CTF CORRECTION NOVACTF ?
MODEL FITTING UCSF Chimera 1.13.1
MODEL FITTING Coot 0.8.9.1
FINAL EULER ASSIGNMENT Dynamo 1.1.333
CLASSIFICATION MATLAB R2018b
RECONSTRUCTION Dynamo 1.1.333
RECONSTRUCTION AV3 ?
MODEL REFINEMENT PHENIX 1.18
MODEL REFINEMENT Coot 0.8.9.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps