7CYC | pdb_00007cyc

Cryo-EM structures of Alphacoronavirus spike glycoprotein

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5SZS

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.647
f_angle_d	1.024
f_chiral_restr	0.068
f_bond_d	0.006
f_plane_restr	0.006

Sample
HCoV-229E spike trimer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	36846
Reported Resolution (Å)	3.21
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (5SZS)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation coefficient
Overall B Value	100
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	18000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM	3-6-11
CTF CORRECTION	CTFFIND	4
MODEL FITTING	UCSF Chimera	1.13
MODEL REFINEMENT	PHENIX	1.14-3260
INITIAL EULER ASSIGNMENT	cryoSPARC	v2.14.2
FINAL EULER ASSIGNMENT	cryoSPARC	v2.14.2
CLASSIFICATION	cryoSPARC	v2.14.2
RECONSTRUCTION	cryoSPARC	v2.14.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		403347