7LAB

Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1052


ELECTRON MICROSCOPY

Starting Model(s)

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

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.219
f_angle_d1.888
f_chiral_restr0.223
f_bond_d0.013
f_plane_restr0.013
Sample
Severe acute respiratory syndrome-related coronavirus spike glycoprotein in complex with RBD antibody DH1052
Sample Components
Spike glycoprotein
Antibody DH1052
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles143411
Reported Resolution (Å)2.97
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (6VXX)
Refinement Space
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)66.71
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon
CTF CORRECTIONcryoSPARC
MODEL FITTINGISOLDE
MODEL FITTINGPHENIX
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION