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Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SXT in silico model SwissModel 6BPB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.3575 f_angle_d 0.9358 f_chiral_restr 0.0512 f_plane_restr 0.0128 f_bond_d 0.0033
Sample SARS-CoV-2 spike trimer in complex with the antibody MO176-117
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 292399 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7SXT) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 14.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 2000 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 PARTICLE SELECTION cryoSPARC 3.3.1 IMAGE ACQUISITION EPU 3.4 CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.21rc1_5109
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2768736