7Y38

Molecular architecture of the chikungunya virus replication complex


ELECTRON MICROSCOPY

Starting Model(s)

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

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.4093
f_angle_d0.507
f_chiral_restr0.0406
f_plane_restr0.0048
f_bond_d0.002
Sample
Alphavirus Replication Complex
Sample Components
nsP1 dodecameric ring
nsP4 RdRp; docked within nsP1 central cavity
nsP2 helicase-protease; docked on top of viral complex with synthetic RNA bound
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Detailswait 45s, blot 2s at force -2
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles132510
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7DOP)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation Coefficient
Overall B Value63.66
Fitting Procedure
DetailsChimeraX was used to fit the 7DOP ring and built/refined using coot/phenix.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)34
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.1
PARTICLE SELECTIONTopaz2.5.0
IMAGE ACQUISITIONEPU2.14
CTF CORRECTIONcryoSPARC3.3.1
MODEL FITTINGUCSF ChimeraX1.3
INITIAL EULER ASSIGNMENTcryoSPARC3.3.1
FINAL EULER ASSIGNMENTcryoSPARC3.3.1
CLASSIFICATIONcryoSPARC3.3.1
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.2
MODEL REFINEMENTCoot0.9.5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2261181template-based picking and neural-network trained TOPAZ picking