7TCC

Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies A19-46.1 and B1-182.1


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7MM0 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.305
f_angle_d0.654
f_chiral_restr0.046
f_plane_restr0.005
f_bond_d0.004
Sample
SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-46.1
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot for 2-3.5 seconds before plugging.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles46244
Reported Resolution (Å)3.86
Resolution MethodFSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (7MM0)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeOTHER
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONcryoSPARC2.15
MODEL FITTINGCoot0.93
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC2.15
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION