6XCN

Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.696
f_angle_d0.828
f_chiral_restr0.051
f_bond_d0.011
f_plane_restr0.005
Sample
SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105
Sample Components
SARS-CoV-2 spike glycoprotein 2P trimer
neutralizing antibody C105 Fab
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 microliters added, blotted for 3 s with 0 blot force
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles14119
Reported Resolution (Å)3.66
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1 (6VYB)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value90
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
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 DetailsCollected with 3x3 pattern and beam image shift
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX1.17
INITIAL EULER ASSIGNMENTcryoSPARC2.14.2
FINAL EULER ASSIGNMENTcryoSPARC2.14.2
CLASSIFICATIONcryoSPARC2.14.2
RECONSTRUCTIONcryoSPARC2.14.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION