8XUZ

Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8IOU 
experimental modelPDB 8IOV 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.471
f_angle_d0.441
f_chiral_restr0.042
f_plane_restr0.004
f_bond_d0.002
Sample
SARS-CoV-2 XBB1.5 spike glycoprotein with ACE2
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 Particles82961
Reported Resolution (Å)3.05
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (8IOU, 8IOV)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)51
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 CS
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 SELECTIONcryoSPARC4.3.1
CTF CORRECTIONcryoSPARC4.3.1
MODEL FITTINGUCSF Chimera1.16
MODEL REFINEMENTCoot0.9.8.7
MODEL REFINEMENTPHENIX1.20.1
INITIAL EULER ASSIGNMENTcryoSPARC4.3.1
FINAL EULER ASSIGNMENTcryoSPARC4.3.1
CLASSIFICATIONcryoSPARC4.3.1
RECONSTRUCTIONcryoSPARC4.3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION3446627