8DW3

Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR16m, and two antibody Fabs, S309 and CR3022


ELECTRON MICROSCOPY

Starting Model(s)

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

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.724
f_angle_d0.921
f_chiral_restr0.047
f_bond_d0.013
f_plane_restr0.008
Sample
DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles37197
Reported Resolution (Å)4.26
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (7BNO)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCC
Overall B Value134
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)40.2
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1250
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONcryoSPARC3.3.1
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX1.20
INITIAL EULER ASSIGNMENTcryoSPARC3.3
RECONSTRUCTIONcryoSPARC3.3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION4115887