Experiment: 7SGD

Lassa virus glycoprotein construct(Josiah GPCysR4) recovered from GPC-I53-50 nanoparticle by localized reconstruction

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VK2

Sample
Lassa virus glycoprotein construct(Josiah GPCysR4) recovered from GPC-I53-50 nanoparticle

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot time 4s, Wait time 10s, Blot force 0

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	124891
Reported Resolution (Å)	3.97
Resolution Method	FSC 0.143 CUT-OFF
Other Details	C3 symmetry used for refinement. Solvent mask applied.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (5VK2)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	50.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	1600
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	29000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	2
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	RosettaEM
MODEL REFINEMENT	Coot

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1728229	This is the number of GPCysR4 trimer subparticles extracted from the GPC-I53-50 nanoparticle by localized reconstruction: 86,411 nanoparticles X 20 = 1728229.