9BNE | pdb_00009bne

SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M0J
experimental model	PDB	6VXX

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.567
f_angle_d	0.49
f_chiral_restr	0.042
f_bond_d	0.004
f_plane_restr	0.003

Sample
Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A antagonist
Sample Components
Trimeric T3A antagonist
SARS-CoV-2 spike HexaPro protein trimer

Specimen Preparation
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	225636
Reported Resolution (Å)	3.43
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6M0J, 6VXX)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial fitting done by superposition of three components of 6M0J (complex of ACE2 and RBD of SARS-CoV-2 spike protein) onto each of the three RBDs of 6VXX (full SARS-CoV-2 spike hexapro protein trimer)

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	3000
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
PARTICLE SELECTION	cryoSPARC
CTF CORRECTION	cryoSPARC
MODEL FITTING	PyMOL
MODEL FITTING	Coot
MODEL FITTING	PHENIX
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch motion correction and Patch CTF applied after Import Movies and before Blob Picker	1616068	Automated Blob Picker Diameter 150 - 300