7B3D

Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with AMP at position -4 (structure 3)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YYT 
Sample
SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing AMP at position -4.
Sample Components
SARS-CoV-2 RNA-dependent RNA polymerase nsp12
SARS-CoV-2 nsp7 and 8
DNA and RNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles819273
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsM was used
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6YYT)
Refinement SpaceREAL
Refinement ProtocolOTHER
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)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeOTHER
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details30 deg tilt.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp1.0.7
IMAGE ACQUISITIONSerialEM3.8
CTF CORRECTIONWarp1.0.7
MODEL FITTINGCoot0.9
MODEL REFINEMENTPHENIX1.18
CLASSIFICATIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1767915