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Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZGE
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.6 f_angle_d 0.552 f_chiral_restr 0.046 f_bond_d 0.004 f_plane_restr 0.004
Sample Stabilised SARS-CoV-2 spike ectodomain trimer bound to one P008_056 Fab Sample Components Stabilised SARS-CoV-2 spike ectodomain trimer P008_056 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 78291 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6ZGE) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details in addition to the spike: 6APC and 6PHB were used as templates for the heavy and light chains of the Fab respectively
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 51
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING UCSF Chimera RECONSTRUCTION cryoSPARC 2 MODEL REFINEMENT PHENIX 1.19rc5-4047
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION