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)
TypeSourceAccession CodeDetails
experimental modelPDB 7SBK 
experimental modelPDB 6XR8 
Sample
Severe acute respiratory syndrome coronavirus 2
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentGATAN CRYOPLUNGE 3
Cryogen NameNITROGEN
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles45252
Reported Resolution (Å)4.39
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1 (7SBK, 6XR8)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value118.79
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1.0
CTF CORRECTIONRELION3.1.0
MODEL FITTINGCoot0.9.6
MODEL REFINEMENTPHENIX1.20.1
INITIAL EULER ASSIGNMENTRELION3.1.0
FINAL EULER ASSIGNMENTRELION3.1.0
RECONSTRUCTIONRELION3.1.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTFs are applied to the projections of the map during 3D classification and 3D refinement.674792Initial 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.