8J26

CryoEM structure of SARS CoV-2 RBD and Aptamer complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KGJ 
experimental modelPDB 6XDG 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d32.628
f_angle_d1.242
f_chiral_restr0.042
f_bond_d0.003
f_plane_restr0.002
Sample
RBD_Fab_AM032-4_AM047-6 complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details2.5 ul of samples placed on grid before plunge frozen with 5s blot time
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles212000
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsFinal map generated using 3D Flex reconstruction following non-uniform refinement
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7KGJ, 6XDG, 6XDG)
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)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.73
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification105000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.1.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.1.1
MODEL FITTINGUCSF Chimera1.16
MODEL REFINEMENTPHENIX1.21rc1_4895:
MODEL REFINEMENTCoot0.9.6 EL
INITIAL EULER ASSIGNMENTcryoSPARC4.1.1
FINAL EULER ASSIGNMENTcryoSPARC4.1.1
CLASSIFICATIONcryoSPARC4.1.1
RECONSTRUCTIONcryoSPARC4.1.1 and 4.2.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1938408Particles picked using TOPAZ train