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Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C144
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 15.257 f_angle_d 0.579 f_chiral_restr 0.046 f_bond_d 0.003 f_plane_restr 0.003
Sample Ternary complex of SARS-CoV-2 S 6P trimer with human neutralizing antibody Fab fragment C144 Sample Components SARS-CoV-2 S 2P glycoprotein neutralizing antibody Fab fragment C144
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3s blot
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 212876 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (6XKL) 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) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 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 3.8 CTF CORRECTION cryoSPARC 2.15 MODEL FITTING UCSF Chimera 1.13 INITIAL EULER ASSIGNMENT cryoSPARC 2.15 FINAL EULER ASSIGNMENT cryoSPARC 2.15 CLASSIFICATION cryoSPARC 2.15 RECONSTRUCTION cryoSPARC 2.15 MODEL REFINEMENT PHENIX 1.18
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION