9CVH | pdb_00009cvh

Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1RBD UP, State-2


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KRR 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.6022
f_angle_d0.4861
f_chiral_restr0.0482
f_plane_restr0.0033
f_bond_d0.0032
Sample
SARS-CoV-2 Spike protein Ectodomain with Internal tag
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles92764
Reported Resolution (Å)2.76
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7KRR)2
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)43.97
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification16500
Calibrated Magnification191780
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONcryoSPARC
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION320507