8GS6

Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7UB0 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.7294
f_angle_d0.5893
f_chiral_restr0.0535
f_plane_restr0.0044
f_bond_d0.0036
Sample
SARS-COV-2 BA.2.75 spike glycoprotein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblotting time 5 s and blotting force 5.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles139418
Reported Resolution (Å)2.86
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7UB0)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC3.3.1
MODEL FITTINGUCSF Chimera1.15
INITIAL EULER ASSIGNMENTcryoSPARC3.3.1
FINAL EULER ASSIGNMENTcryoSPARC3.3.1
CLASSIFICATIONcryoSPARC3.3.1
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION754589