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Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B62 experimental model PDB 7K4N experimental model PDB 6M0J
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.896 f_angle_d 0.713 f_chiral_restr 0.051 f_plane_restr 0.007 f_bond_d 0.003
Sample SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment Sample Components SARS-CoV-2 spike glycoprotein 87G7 antibody Fab fragment
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 133550 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (7B62, 7K4N, 7K4N, 6M0J) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 51.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU 2 MODEL FITTING UCSF Chimera 1.15.0 MODEL FITTING Coot 0.9.6 FINAL EULER ASSIGNMENT cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 934811 313636 particles were picked from 1331 images from 0.02% FOM dataset and 621175 particles were picked from 2500 images without FOM.