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BG505 SOSIP trimer reconstructed from a designed tetrahedral nanoparticle BG505 SOSIP-T33_dn2
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Lauryl maltose neopentyl glycol (LMNG) at a final concentration of 0.005 mM was added to the nanoparticle sample (4.0 mg/mL) and 3 uL was immediately ...
Lauryl maltose neopentyl glycol (LMNG) at a final concentration of 0.005 mM was added to the nanoparticle sample (4.0 mg/mL) and 3 uL was immediately loaded onto plasma-cleaned Quantifoil R 2/1 holey carbon copper grid (Cu, 400-mesh, Quantifoil Micro Tools GmbH).
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
52939
Reported Resolution (Å)
4.5
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
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TALOS ARCTICA
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
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
Gctf
MODEL FITTING
UCSF Chimera
INITIAL EULER ASSIGNMENT
RELION
3.0
FINAL EULER ASSIGNMENT
RELION
3.0
CLASSIFICATION
RELION
3.0
RECONSTRUCTION
RELION
3.0
MODEL REFINEMENT
Rosetta
MODEL REFINEMENT
Coot
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING ONLY
142084
Starting number of BG505 SOSIP-T33_dn2 nanoparticles was 35,521. BG505 SOSIP subparticles were extracted using LocalRec v1.2.0. There are 4 trimeric BG505 SOSIP subparticles per one T33_dn2 nanoparticle, making a total of 142,084 starting subparticles.