3J40

Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling

ELECTRON MICROSCOPY

Sample
Bacteriophage epsilon15

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details	Blot before plunging into liquid ethane (FEI VITROBOT MARK II).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	14000
Reported Resolution (Å)	4.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The gold standard definition for the resolution estimate was adopted whereby the particle images were split into two subsets at the onset of image pro ...	The gold standard definition for the resolution estimate was adopted whereby the particle images were split into two subsets at the onset of image processing and the datasets were individually reconstructed and then combined after determination of the resolution estimate. Independent initial models were built de novo and used for the subsequent particle refinements in each of the two subsets of particle images. The Fourier Shell Correlation (FSC) between the two independently determined reconstructions was computed and indicated a resolution of 4.5 Angstrom using the 0.143 threshold for the combined dataset. (Single particle details: Individual particles (720x720 pixels) were first automatically selected using the ethan method followed by manual screening using the EMAN boxer program. A total of 54161 particles were selected for initial processing. The selected particles within a micrograph were incoherently averaged to generate 2D power spectra for contrast transfer function (CTF) parameter determination. CTF parameters were first automatically estimated and then visually verified using the EMAN1 ctfit program. Defocus values range from 0.5 to 2.5 um. The data set was divided into two data subsets for the following reconstruction steps. The particle images were first binned 4x for initial model building and initial determination of orientation and center parameters. The initial model was built de novo by iterative refinement of a subset of 300 particles randomly selected from the half data set with randomly assigned initial orientations. The initial orientations of all particles in each of the half data sets were determined using the EMAN1 projection matching program classesbymra with an angular projection step size of 3 degrees. The orientations were then refined to higher accuracy using the program jalign, which is based on simplex optimization of matching between the particle image and model projections. The particle orientation parameters were then transferred to particles binned at 2x and ultimately to particles without binning for further refinements. In the last stage of refinement, magnification, astigmatism, and defocus parameters were also included. 3D maps with icosahedral symmetry enforcement were reconstructed using a newly developed program, j3dr, using the EMAN2 library and parallelized with message passing interface (MPI) to speed up the reconstruction process. These steps were iterated until the refinement converged. The map for each data subset was reconstructed from ~7000 particles by removing particles with poor alignment scores and unstable alignment parameters. The resolution of the map was evaluated using the Fourier Shell Correlation (FSC). Only the icosahedral shell region was included in this FSC analysis by masking out the external background noises and the internal DNA densities using soft masks with a half width of 6 Angstrom. The final map of the entire dataset was then built from ~14000 particles by combining these two subsets of particles.) (Single particle--Applied symmetry: I)
Refinement Type	HALF-MAPS REFINED INDEPENDENTLY
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	17

Imaging Experiment	1
Date of Experiment	2007-01-03
Temperature (Kelvin)	81
Microscope Model	JEOL 3200FSC
Minimum Defocus (nm)	400
Maximum Defocus (nm)	2700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	4.1
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	JEOL 3200FSC CRYOHOLDER
Nominal Magnification	50000
Calibrated Magnification	53361
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
RECONSTRUCTION	EMAN	1
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	jspr

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	per particle

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.