7LYL

South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the RBD-down conformation


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JMO 
experimental modelPDB 7KDK 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.012
f_angle_d1.7
f_chiral_restr0.092
f_bond_d0.013
f_plane_restr0.013
Sample
South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles65713
Reported Resolution (Å)3.72
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (7JMO, 7KDK)
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)51.16
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 Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCoot
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTISOLDE
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION