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CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VYB experimental model PDB 7EAN
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.85 f_angle_d 1.868 f_chiral_restr 0.124 f_plane_restr 0.017 f_bond_d 0.013
Sample Severe acute respiratory syndrome-related coronavirus spike glycoprotein in complex with RBD antibody DH1042 Sample Components Spike glycoprotein Antibody DH1042
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 175460 Reported Resolution (Å) 3.42 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6VYB, 6VYB, 6VYB, 7EAN, 7EAN, 7EAN) Refinement Space Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 54.02
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 750 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING ISOLDE MODEL FITTING PHENIX MODEL FITTING UCSF Chimera MODEL REFINEMENT ISOLDE MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION