7Y71

SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XKL 
experimental modelPDB 6N16 
Sample
SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles198525
Reported Resolution (Å)3.12
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNon-uniform refinement in cryoSPARC
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6XKL, 6N16, 6N16)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)31.6
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp1.0.9
IMAGE ACQUISITIONSerialEM3.8.6
CTF CORRECTIONCTFFIND4.1.14
MODEL FITTINGUCSF Chimera1.16
MODEL FITTINGCoot0.8.9.2-pre
INITIAL EULER ASSIGNMENTRELION4.0-beta-2-commit-543db0
FINAL EULER ASSIGNMENTcryoSPARC3.3.1+220215
RECONSTRUCTIONcryoSPARC3.3.1+220215
MODEL REFINEMENTCoot0.8.9.2-pre
MODEL REFINEMENTPHENIX1.20.1-4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION402809