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Cryo-EM structure of the HCoV-229E spike glycoprotein
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 15.7235 f_angle_d 2.0006 f_chiral_restr 0.1158 f_bond_d 0.0168 f_plane_restr 0.0152
Sample Human coronavirus 229E spike glycoprotein
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument GATAN CRYOPLUNGE 3 Cryogen Name ETHANE-PROPANE Sample Vitrification Details Blot for 13 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 71350 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (5SZS) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Manual 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 Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 42.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1.10 MODEL FITTING UCSF Chimera 1.12 RECONSTRUCTION cryoSPARC 2.90 MODEL REFINEMENT PHENIX 1.16RC1-3535
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION