6U7H

Cryo-EM structure of the HCoV-229E spike glycoprotein


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5SZS 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.7235
f_angle_d2.0006
f_chiral_restr0.1158
f_bond_d0.0168
f_plane_restr0.0152
Sample
Human coronavirus 229E spike glycoprotein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentGATAN CRYOPLUNGE 3
Cryogen NameETHANE-PROPANE
Sample Vitrification DetailsBlot for 13 seconds before plunging
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles71350
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1 (5SZS)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsManual model building was done in COOT and ChimeraX/ISOLDE. A homology model based on PDB:5SZS was used as a reference during model building.
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)42.7
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 CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1.10
MODEL FITTINGUCSF Chimera1.12
RECONSTRUCTIONcryoSPARC2.90
MODEL REFINEMENTPHENIX1.16RC1-3535
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION