Experiment: 7Y6D

Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7SBK
experimental model	PDB	6XR8

Sample
Severe acute respiratory syndrome coronavirus 2

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	NITROGEN
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	45252
Reported Resolution (Å)	4.39
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (7SBK, 6XR8)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value	118.79
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.1.0
CTF CORRECTION	RELION	3.1.0
MODEL FITTING	Coot	0.9.6
MODEL REFINEMENT	PHENIX	1.20.1
INITIAL EULER ASSIGNMENT	RELION	3.1.0
FINAL EULER ASSIGNMENT	RELION	3.1.0
RECONSTRUCTION	RELION	3.1.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTFs are applied to the projections of the map during 3D classification and 3D refinement.	674792	Initial micrographs were deconvolved using Warp, and 7,950 spikes were manually picked from 474 micrographs for training Topaz neural network. The trained Topaz neural network was used to automatically pick the spikes. 674,792 particles were auto-picked by Topaz.