8OPN

Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (1-up state)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOther6nzk 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.54
f_angle_d0.882
f_chiral_restr0.055
f_plane_restr0.006
f_bond_d0.004
Sample
Trimeric spike glycoprotein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles36048
Reported Resolution (Å)4.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCross-correlation coefficient
Overall B Value114
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)46
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.2
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC3.3.2
MODEL FITTINGUCSF Chimera1.16
MODEL FITTINGUCSF ChimeraX1.5
MODEL REFINEMENTPHENIX1.19.2-4158
MODEL REFINEMENTCoot0.9.8.1
INITIAL EULER ASSIGNMENTcryoSPARC4.1
FINAL EULER ASSIGNMENTcryoSPARC4.1
CLASSIFICATIONcryoSPARC4.1
RECONSTRUCTIONcryoSPARC4.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION956697