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Structure of the SARS-CoV-2 S 6P trimer in complex with the cow antibody 99 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SC1 experimental model PDB 6E9H
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.8727 f_angle_d 0.5558 f_chiral_restr 0.0435 f_plane_restr 0.0035 f_bond_d 0.0022
Sample SARS-CoV-2 S 6P in complex with 99 Fab Sample Components Severe acute respiratory syndrome coronavirus 2 spike glycoprotein 99 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 161249 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7SC1, 6E9H) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 90 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 v3.3.25 MODEL REFINEMENT PHENIX 1.21.2_5419 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC v3.3.25 INITIAL EULER ASSIGNMENT cryoSPARC v3.3.25 FINAL EULER ASSIGNMENT cryoSPARC v3.3.25 CLASSIFICATION cryoSPARC v3.3.25 RECONSTRUCTION cryoSPARC v3.3.25
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1016227