4ADX | pdb_00004adx

The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CC2
experimental model	PDB	3O58
experimental model	PDB	4A17
experimental model	PDB	4A19

Sample
50S RIBOSOMAL SUBUNIT IN COMPLEX WITH ARCHAEAL IF6

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	MANUAL PLUNGING INTO LIQUID ETHANE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	70364
Reported Resolution (Å)	6.6
Resolution Method
Other Details	THIS ENTRY IS A MODEL OF THE METHANOTHERMOBACTER THERMAUTOTROPHICUS 50S-AIF6 COMPLEX AND WAS GENERATED BY RIGID BODY DOCKING OF HIGH RESOLUTION STRUCTURES INTO THE EXPERIMENTAL CRYO-EM MAP EMD-2012.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3CC2, 3O58, 4A17, 4A19)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI 20
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	62000
Calibrated Magnification	83000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	IMAGIC	5
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	BY CCD FRAME