Experiment: 6ZOW

SARS-CoV-2 spike in prefusion state

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VSB
experimental model	PDB	6VYB
experimental model	PDB	6YLA

Sample
Spike homotrimer in prefusion state

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	203000
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6VSB, 6VSB, 6VSB, 6VSB, 6VYB, 6VYB, 6VYB, 6VYB, 6YLA)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial models 6VSB and 6VYB were used for flexible fitting, whereas 6YLA was used for rigid fitting of the RBD domain of chain A, that we have called ...	Initial models 6VSB and 6VYB were used for flexible fitting, whereas 6YLA was used for rigid fitting of the RBD domain of chain A, that we have called a in the final structure.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	36

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
MODEL FITTING	PHENIX
MODEL FITTING	CCP4 package
MODEL REFINEMENT	PHENIX	1.17
CLASSIFICATION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION