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Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)
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 10.529 f_angle_d 0.688 f_chiral_restr 0.047 f_bond_d 0.008 f_plane_restr 0.004
Sample SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105 Sample Components SARS-CoV-2 spike glycoprotein 2P trimer neutralizing antibody C105 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 microliters added, blotted for 3 s with 0 blot force
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 58873 Reported Resolution (Å) 3.42 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 90 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 Collected with 3x3 pattern and beam image shift
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC 2.14.2 FINAL EULER ASSIGNMENT cryoSPARC 2.14.2 CLASSIFICATION cryoSPARC 2.14.2 RECONSTRUCTION cryoSPARC 2.14.2 MODEL REFINEMENT PHENIX 1.17
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION