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Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR16m, and two antibody Fabs, S309 and CR3022
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BNO
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.724 f_angle_d 0.921 f_chiral_restr 0.047 f_bond_d 0.013 f_plane_restr 0.008
Sample DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
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 37197 Reported Resolution (Å) 4.26 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7BNO) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target CC Overall B Value 134 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1250 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.20 INITIAL EULER ASSIGNMENT cryoSPARC 3.3 RECONSTRUCTION cryoSPARC 3.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4115887