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Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XKL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.755 f_angle_d 0.978 f_chiral_restr 0.134 f_bond_d 0.005 f_plane_restr 0.005
Sample Ternary complex of BG1-22 Fab bound to SARS-CoV-2 spike trimer Sample Components SARS-CoV-2 spike trimer BG1-22 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3s blot, 0 blot force
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 71104 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Model building for Fab-RBD was done in local refined map. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6XKL) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI ARCTICA Minimum Defocus (nm) 700 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 45000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM v3.8 CTF CORRECTION cryoSPARC 2.14 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.19 INITIAL EULER ASSIGNMENT cryoSPARC 2.14 FINAL EULER ASSIGNMENT cryoSPARC 2.14 CLASSIFICATION cryoSPARC 2.14 RECONSTRUCTION cryoSPARC 2.14
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 756849 Blob picker