4V2T | pdb_00004v2t

Membrane embedded pleurotolysin pore with 13 fold symmetry

ELECTRON MICROSCOPY

Starting Model(s)

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

Sample
PLEUROTOLYSIN PORE IN LIPOSOMES

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY - 80, INSTRUMENT- FEI VITROBOT MARK III, METHOD- PLEUROTOLYSIN A WAS FIRST ADDED TO SPHINGOMYELIN-CHOLEST ...	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY - 80, INSTRUMENT- FEI VITROBOT MARK III, METHOD- PLEUROTOLYSIN A WAS FIRST ADDED TO SPHINGOMYELIN-CHOLESTEROL LIPOSOMES AT A MOLAR RATIO OF 1 TO 2000 PROTEIN TO LIPID IN THE ABOVE BUFFER. AFTER 5 MIN INCUBATION AT ROOM TEMPERATURE, PLEUROTOLYSIN B WAS ADDED TO THE MIXTURE AT A MOLAR RATIO OF 1 TO 2 TO PLEUROTOLYSIN A. THE MIXTURE WAS INCUBATED AT 40C OR ROOM TEMPERATURE FOR 30 MIN AFTER WHICH 3. 5 UL WERE PLACED ON NEGATIVELY GLOW DISCHARGED LACEY GRIDS AND VITRIFIED IN LIQUID ETHANE USING A VITROBOT. BLOTTING WAS CARRIED OUT AT 36C AND 80 PERCENT HUMIDITY.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	8700
Reported Resolution (Å)	11
Resolution Method
Other Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2793. (DEPOSITION ID: 12292).
Refinement Type
Symmetry Type	POINT
Point Symmetry	C13

Map-Model Fitting and Refinement
Id	1 (4OEB)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	METHOD--FLEXIBLE

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2011-01-19
Temperature (Kelvin)	94
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	800
Maximum Defocus (nm)	3200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.3
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	59000
Calibrated Magnification	76148
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Flex-EM
MODEL FITTING	MODELLER
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	ESTIMATED WITH CTFFIND3, THEN PHASES FLIPPED FOR EACH 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.