7DZW

Apo spike protein from SARS-CoV2


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KEB 
Sample
Spike glycoprotein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles120442
Reported Resolution (Å)3.45
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7KEB)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation
Overall B Value
Fitting Procedure
DetailsThe protein was homology modeled using MODELLER software. Then, the model was fitted into cryo-EM map.
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)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.0452
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 CORRECTION