ELECTRON MICROSCOPY

Sample

Monomeric Spike glycoprotein ectodomain from SARS-CoV-2 in complex with a neutralising antibody P008_60

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details blotted for 3 to 4 sec before plunging
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 166619
Reported Resolution (Å) 4.31
Resolution Method FSC 0.143 CUT-OFF
Other Details Non Uniform refinement in cryoSPARC
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol OTHER
Refinement Target Correlation coefficient
Overall B Value 81
Fitting Procedure ?
Details The atomistic models of monomeric SARS-CoV-2 S1 protein and a Fab molecule, extracted from PDB entries 7A92 and 5WI9, were docked in the cryo-EM map using Chimera. The NTD and the RBD of the spike subunit were replaced with the crystal structures from PDB entries 7B62 and 7OAO, respectively. Guided by the cryo-EM map, the model was adjusted and extended interactively in Coot and refined using phenix.real_space_refine.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 700
Maximum Defocus (nm) 3600
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 ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION Gautomatch 0.53
IMAGE ACQUISITION EPU ?
CTF CORRECTION Gctf 1.06
MODEL FITTING UCSF Chimera ?
CLASSIFICATION RELION 3.1
RECONSTRUCTION cryoSPARC 2
MODEL REFINEMENT PHENIX 4213
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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