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SARS-CoV-2 Omicron-BA.2 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron-BA.2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KDK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.053 f_angle_d 0.466 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Sample SARS-CoV-2 S-GSAS-Omicron-BA.2 Spike Ectodomain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 411890 Reported Resolution (Å) 3.31 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7KDK) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 54.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2600 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION Coot RECONSTRUCTION ISOLDE RECONSTRUCTION PHENIX MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION