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Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1 that targets the receptor-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LRT
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.2 f_angle_d 0.536 f_chiral_restr 0.047 f_plane_restr 0.004 f_bond_d 0.003
Sample SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot for 4 seconds before plugging.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 208776 Reported Resolution (Å) 3.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7LRT) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Iterative refinement and manual model building/adjustment with Phenix and Coot.
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1100 Maximum Defocus (nm) 2100 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 2.15 CTF CORRECTION cryoSPARC 2.15 MODEL FITTING Coot 0.93 MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF of CryoSparc 1531919 Particles after selection of useful 2D classification