5TSL

Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP3 Subunit


ELECTRON MICROSCOPY
Sample
coxsackievirus A16
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1642
Reported Resolution (Å)6.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (4JGY)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsWeighting factor of 0.5 was chosen to weigh the contribution of the cryo-EM map in the molecular dynamic simulation. The simulation started with 20 00 ...Weighting factor of 0.5 was chosen to weigh the contribution of the cryo-EM map in the molecular dynamic simulation. The simulation started with 20 000 steps of minimization followed by 100 000 steps of molecular dynamics before converging.
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2000
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.05
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification57000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONjspr
CTF CORRECTIONjspr
MODEL FITTINGNAMD2.1
INITIAL EULER ASSIGNMENTjspr
FINAL EULER ASSIGNMENTjspr
CLASSIFICATIONjspr
RECONSTRUCTIONjspr
MODEL REFINEMENTNAMD2.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY