7DZY

Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KEW 
experimental modelPDB 5K8M 
Sample
Spike protein of SARS-CoV2 with Fab fragment of enhancing antibody 2490
Sample Components
Spike glycoprotein
Fab fragment of enhancing antibody 2490
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles131312
Reported Resolution (Å)3.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7KEW)2 (5K8M)
Refinement SpaceREALREAL
Refinement ProtocolRIGID BODY FITRIGID BODY FIT
Refinement Targetcorrelationcorrelation
Overall B Value
Fitting Procedure
DetailsThe protein was homology modeled using MODELLER software. Then, the model was fitted into cryo-EM map as a rigid body. The loop region of NTD was remo ...The protein was homology modeled using MODELLER software. Then, the model was fitted into cryo-EM map as a rigid body. The loop region of NTD was remodeled using MODELLER.
Variable domains were built by using a BCR modelling software.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.0355
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.0.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC3.0.1
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTcryoSPARC3.0.1
FINAL EULER ASSIGNMENTcryoSPARC3.0.1
CLASSIFICATIONcryoSPARC3.0.1
RECONSTRUCTIONcryoSPARC3.0.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION5177