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SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8H3N in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.7833 f_angle_d 0.5186 f_chiral_restr 0.0451 f_plane_restr 0.0042 f_bond_d 0.002
Sample Complex of spike ectodomain with antibody MO11 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 246238 Reported Resolution (Å) 2.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (8H3N) 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) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 1200 Maximum Defocus (nm) 1600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 60000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.8.2 IMAGE ACQUISITION SerialEM 4.1beta10 CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF ChimeraX 1.6 MODEL REFINEMENT PHENIX 1.21rc1_5109 MODEL REFINEMENT Coot 0.9.8.1 INITIAL EULER ASSIGNMENT RELION 4.0.0 FINAL EULER ASSIGNMENT RELION 4.0.0 RECONSTRUCTION RELION 4.0.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION