4V4N | pdb_00004v4n

Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RHZ
experimental model	PDB	3J21
experimental model	PDB	3J2L
experimental model	PDB	3J20

Sample
Methanococcus jannaschii 70S ribosome-SecYEbeta complex
Sample Components
non-translating 70S ribosome
SecYEbeta
transfer RNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	37000
Reported Resolution (Å)	9
Resolution Method	FSC 0.5 CUT-OFF
Other Details	Final map calculated as an average of 6 different refinements in EMAN2 with different parameters. Resolution method was FSC at 0.5 cut-off using a co ...	Final map calculated as an average of 6 different refinements in EMAN2 with different parameters. Resolution method was FSC at 0.5 cut-off using a comparison between experimental map and a map of the docked ribosomal models calculated at 7 Angstrom resolution with EMAN.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	Refinement Space	Refinement Protocol	Refinement Target	Overall B Value	Fitting Procedure	Details
1 (1RHZ, 1RHZ, 1RHZ)	REAL	FLEXIBLE FIT				REFINEMENT PROTOCOL--FLEXIBLE
2 (3J21)	REAL	FLEXIBLE FIT				REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Docked with ...	REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Docked with Chimera and fit with MDFF. Chains omitted- 1(el 1-77), 6(L83-1), 4(L83-2), c(L33e). Chains truncated- a(L31e) 78-85, W(L29) 67-72, C(L3) 103-125.
3 (3J2L)	REAL	FLEXIBLE FIT				REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Regions omi ...	REFINEMENT PROTOCOL--FLEXIBLE DETAILS--Regions omitted- rRNA chain 1 [1-6, 3047-3049 5 and 3 ends 23S], 150-163, 750-756, 1311-1321, 2904-2942 (ES).
4 (3J20)	REAL	FLEXIBLE FIT				REFINEMENT PROTOCOL--FLEXIBLE

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

Imaging Experiment	1
Date of Experiment	2008-04-10
Temperature (Kelvin)	93
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
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, data collected manually

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	1
RECONSTRUCTION	EMAN	2

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.