3J45 | pdb_00003j45

Structure of a non-translocating SecY protein channel with the 70S ribosome

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I2P
experimental model	PDB	3J01

Sample
non-translating E coli ribosome-SECYEG channel complex
Sample Components
non-translating 70S ribosome
SecYEbetaG

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Blot 1 second before plunging into liquid ethane (HOMEMADE PLUNGER).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	39000
Reported Resolution (Å)	9.5
Resolution Method	OTHER
Other Details	CTF correction was done on untilted and 30 degree tilted images. Resolution method was comparison of 3D map with calculated map of docked ribosomal co ...	CTF correction was done on untilted and 30 degree tilted images. Resolution method was comparison of 3D map with calculated map of docked ribosomal components, with the second map made with EMAN at 7 Angstrom resolution.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2I2P)	2 (3J01)
Refinement Space	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--FLEXIBLE	REFINEMENT PROTOCOL--FLEXIBLE

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2006-04-10
Temperature (Kelvin)	93
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)	30
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	50000
Calibrated Magnification	51000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	low dose imaging with manual data collection

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	1

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

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.