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Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C135
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VYB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.933 f_angle_d 0.752 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.005
Sample Ternary complex of SARS-CoV-2 S 2P glycoprotein with Fab fragments of the human neutralizing antibody C135 Sample Components SARS-CoV-2 S 2P glycoprotein neutralizing antibody C135
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3s blot, 0 blot force
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 101114 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6VYB) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target correlation coefficient 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 TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 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 IMAGE ACQUISITION SerialEM 3.8 CTF CORRECTION cryoSPARC 2.15 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.17 INITIAL EULER ASSIGNMENT cryoSPARC 2.15 FINAL EULER ASSIGNMENT cryoSPARC 2.15 CLASSIFICATION cryoSPARC 2.15 RECONSTRUCTION cryoSPARC 2.15
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 634621