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Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KLS
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.173 f_angle_d 0.548 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.002
Sample SARS-CoV-2 spike of the Omicron Variant of Concern
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot for 2-3.5 seconds before plugging.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 266434 Reported Resolution (Å) 3.29 Resolution Method FSC 0.5 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7KLS) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION cryoSPARC 2.15 MODEL FITTING Coot 0.93 MODEL REFINEMENT PHENIX 1.19 RECONSTRUCTION cryoSPARC 2.15
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION