5TSK | pdb_00005tsk

Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JGY

Sample
coxsackievirus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 2 seconds before plunging

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1642
Reported Resolution (Å)	6.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (4JGY)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	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 Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	0.005
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	57000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Objective lens astigmatism was corrected at 75000 magnification

EM Software
Task	Software Package	Version
PARTICLE SELECTION	jspr
CTF CORRECTION	jspr
MODEL FITTING	NAMD	2.1
INITIAL EULER ASSIGNMENT	jspr
FINAL EULER ASSIGNMENT	jspr
CLASSIFICATION	jspr
RECONSTRUCTION	jspr
MODEL REFINEMENT	NAMD	2.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY