ELECTRON MICROSCOPY

Sample

Citrus sudden death-associated virus

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details blot for 8 seconds before plunging with -2mm off set
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 12732
Reported Resolution (Å) 3.4
Resolution Method FSC 0.143 CUT-OFF
Other Details Relion is used for finial reconstruction
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Ab initio model of an ASU is built in Coot and the corresponding density map is then cut out using UCSF Chimera. The model is then refined in Phenix.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 60
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS GLACIOS
Minimum Defocus (nm) 600
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 45000
Calibrated Magnification 56818
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details Direct alignment is done from microscope side, then COMA free alignment and CTF based astigmatism correction is done using SerialEM.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 3.1
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION RELION 3.1
MODEL FITTING UCSF Chimera ?
MODEL REFINEMENT PHENIX 1.19.2
INITIAL EULER ASSIGNMENT RELION 3.1
FINAL EULER ASSIGNMENT RELION 3.1
CLASSIFICATION RELION 3.1
RECONSTRUCTION RELION 3.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?