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BG505-SOSIP reconstructed from the tetrahedral nanoparticle T33_dn10 by subparticle extraction and refinement
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Blotting time varied in the 3-7 s range, Blotting force set to 0, Wait time of 10s.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
84435
Reported Resolution (Å)
4.14
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C3
Map-Model Fitting and Refinement
Id
1 (5CEZ)
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Model refinement was performed by iterating between Rosetta relaxed refinement and manual refinement in Coot.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
49.39
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TALOS ARCTICA
Minimum Defocus (nm)
600
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
OTHER
Nominal Magnification
36000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
IMAGE ACQUISITION
Leginon
CTF CORRECTION
RELION
3.0
MODEL FITTING
UCSF Chimera
MODEL REFINEMENT
Rosetta
INITIAL EULER ASSIGNMENT
RELION
3.0
FINAL EULER ASSIGNMENT
RELION
3.0
CLASSIFICATION
RELION
3.0
RECONSTRUCTION
RELION
3.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING ONLY
324420
81105 T33_dn10 tetrahedral nanoparticles (each carrying 4 copies of BG505-SOSIP antigen) have been 3D aligned in Relion. Particles have been aligned and refined using tetrahedral symmetry. Localized reconstruction v1.2 was then applied to extract the BG505-SOSIP trimeric subparticles, resulting in a total of 324420 starting particles. The full nanoparticle reconstruction can be found elsewhere (EMD-21185).