ELECTRON MICROSCOPY

Sample

Tick-borne encephalitis virus (strain HYPR) and Fab

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Wait time: 10 s Blot time: 2 s Blot force: -2 Drain time: 0 s
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 9797
Reported Resolution (Å) 3.9
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space RECIPROCAL
Refinement Protocol OTHER
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details An initial model was generated based on the tick-borne encephalitis virus (TBEV) cryo-EM structure (PDB:5O6A) and a homology modle of the Fab 19/1786. The model was rigid-body fitted to the electron density map of the TBEV+Fab 19/1786 using the program Chimera. Subsequently, the structure was manually corrected using the program Coot, followed by real-space refinement in Phenix and reciprocal space refinement in Refmac5.
Data Acquisition
Detector Type FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å2) 22
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3000
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 75000
Calibrated Magnification 75000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION EMAN 2.1
IMAGE ACQUISITION EPU 2
CTF CORRECTION Gctf 1.06
MODEL FITTING UCSF Chimera 1.11
MODEL FITTING Coot 0.8.7
MODEL REFINEMENT PHENIX 1.11
MODEL REFINEMENT REFMAC 5.8.0158
INITIAL EULER ASSIGNMENT RELION 1.4
FINAL EULER ASSIGNMENT RELION 1.4
CLASSIFICATION RELION 1.4
RECONSTRUCTION RELION 1.4
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?