7YH7

SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YYB 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.1108
f_angle_d0.4719
f_chiral_restr0.0427
f_plane_restr0.0043
f_bond_d0.0019
Sample
SARS-CoV-2 spike glycoprotein in complex with NIV-8
Sample Components
SARS-CoV-2 spike glycoprotein
NIV-8 Fab
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblotting time 5 s and blotting force 5.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles13430
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6YYB)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)57
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC3.3.1
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTcryoSPARC3.3.1
FINAL EULER ASSIGNMENTcryoSPARC3.3.1
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION206354