9F9Y | pdb_00009f9y

SARS-CoV-2 BA-2.87.1 Spike ectodomain

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8R1C

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.937
f_angle_d	0.453
f_chiral_restr	0.042
f_bond_d	0.003
f_plane_restr	0.003

Sample
BA-2.87.1 variant SARS-CoV2 S protein

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	37441
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Determined in cryosparc local resolution estimation module.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (8R1C)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Phenix real space refinement with manual checks using coot.

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2600
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	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v.4.3.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	v.4.3.1
MODEL FITTING	Coot
MODEL FITTING	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC	v.4.3.1
CLASSIFICATION	cryoSPARC	v.4.3.1
RECONSTRUCTION	cryoSPARC	v.4.3.1
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Determined using cryoSPARC live patch CTF correction.	504319