3NB3 | pdb_00003nb3

The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QJP
experimental model	PDB	2J1N

Sample
bacteriophage Sf6

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	3232
Reported Resolution (Å)	19
Resolution Method
Other Details	The initial model was the cryoEM map of the related phage P22.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1QJP, 2J1N)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--manual fitting in O coupled with local optimization with UCSF Chimera REFINEMENT PROTOCOL--rigid body

Data Acquisition
Detector Type	GENERIC CCD (2k x 2k)
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2008-07-18
Temperature (Kelvin)	89
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1060
Maximum Defocus (nm)	471
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	4
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	39000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	none