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CryoEM structure of SARS CoV-2 RBD and Aptamer complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KGJ experimental model PDB 6XDG
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 33.298 f_angle_d 1.296 f_chiral_restr 0.041 f_bond_d 0.003 f_plane_restr 0.002
Sample RBD_Fab_AM032_AM047 complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 2.5 ul of samples placed on grid before plunge frozen with 5s blot time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 387000 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Final map generated from 3D flex reconstruction following non-uniform refinement. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7KGJ, 6XDG, 6XDG) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.73 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification 105000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.2 MODEL FITTING UCSF Chimera 1.16 MODEL REFINEMENT PHENIX 1.21rc1_4895: MODEL REFINEMENT Coot 0.9.6 EL INITIAL EULER ASSIGNMENT cryoSPARC 3.3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.3.2 CLASSIFICATION cryoSPARC 4.0.0 RECONSTRUCTION cryoSPARC 4.1.0 and 4.2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5448100 Particles picked using TOPAZ train