ELECTRON MICROSCOPY

Sample

Spike protein (S-6P) in complex with Synthetic nanobody (Sb45)

Specimen Preperation
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 214171
Reported Resolution (Å) 3.02
Resolution Method FSC 0.143 CUT-OFF
Other Details A series of "Ab-initio 3D reconstruction" dividing 2 or 4 subclasses to identify two forms of configurations of S-6P, i.e. one RBD up or two RBD up.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target Correlation Coefficient
Overall B Value 157
Fitting Procedure ?
Details An initial model for S-6P was generated using PDB 6XKL and rigid body fitted into the map using Chimera. The RBD domain (334-528) and Sb45 are taken from 7KGJ which was superimposed onto the S-6P model in PyMol. The NTD domain (14-289) is taken from 7B32 with full sequence and replace that of 6XKL. We have rebuilt and added more glycans (NAGs). We used the real-space refinement in PHENIX including rigid-body refinement. RBD and NTD are subjected to rigid-body refinement. Simulate annealing (SA) runs once at the initial micro-step, local grid search and ADP refinements were included, using the secondary structure restraints.
Data Acquisition
Detector Type GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å2) 56
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 700
Maximum Defocus (nm) 2000
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 47529
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC v3.2.0
IMAGE ACQUISITION SerialEM 3.8.0
CTF CORRECTION cryoSPARC v3.2.0
MODEL FITTING UCSF Chimera 2021
MODEL REFINEMENT PHENIX 1.19.2
CLASSIFICATION cryoSPARC 3.2.0
RECONSTRUCTION cryoSPARC V3.2.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
NONE patch CTF estimation