ELECTRON MICROSCOPY

Sample

VLP fusion sequence expressed in E.coli.

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details 3 ul applied for 30s at room temperature, then 4 - 5 s blot
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 8598
Reported Resolution (Å) 3.4
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 FLEXIBLE FIT
Refinement Target Correlation with the map plus geometry
Overall B Value 111.33
Fitting Procedure ?
Details The 4 protein chains from the original T=4 HBV core shell structure solved by X-ray crystallography (Wynne, Leslie, Crowther, 1999), PDB code 1QGT, representing two independently resolved dimeric spikes, were docked into the map using DockEM, and visualised in UCSF Chimera. Part of the chains near the tips of the spikes did not fit well to the map. This region of the map, corresponding to the major immune dominant region where the inserted NadA epitope was placed, was poorly resolved. Therefore the model region according to the native sequence between, but not including, Leu76 to Arg82 was deleted from all 4 chains. This model was then refined against the map with the phenix.real_space_refine program, using global minimisation, simulated annealing, B-factor refinement, and without non-crystallographic symmetry (NCS) restraints. Default parameters were used for other constraints. The resulting model was re-refined once using the local_grid_search option, with all other parameters left unchanged.
Data Acquisition
Detector Type FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å2) 79
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 2500
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 104167
Calibrated Magnification 100719
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION EMAN2 2.01
IMAGE ACQUISITION EPU ?
CTF CORRECTION EMAN2 2.01
MODEL FITTING DockEM ?
MODEL REFINEMENT PHENIX PHENIX.real-space_refine
INITIAL EULER ASSIGNMENT cryoSPARC v0.65
FINAL EULER ASSIGNMENT cryoSPARC v0.65
CLASSIFICATION cryoSPARC v0.65
RECONSTRUCTION cryoSPARC v0.65
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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