4V5Z | pdb_00004v5z

Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J5E
experimental model	PDB	1VI6
experimental model	PDB	1FJG
experimental model	PDB	1IGV
experimental model	PDB	1I6U
experimental model	PDB	2AVY
experimental model	PDB	1G1X
experimental model	PDB	1RQ6
experimental model	PDB	1K7K

Sample
40S ribosomal subunit in the 80S ribosome-channel complex
Sample Components
40S ribosomal subunit

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	plunge freezing with a custom apparatus at 4C and RH greater than 90 percent

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	78800
Reported Resolution (Å)	8.7
Resolution Method
Other Details	Refinements done in EMAN
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1J5E, 1VI6, 1FJG, 1IGV, 1I6U, 2AVY, 1G1X, 1RQ6, 1K7K)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Rigid body fitting and best visual fit using the program O for RNA. For the proteins DOPE score and other statistical techniques were used to evaluate the best fold and a local exhaustive exploration of Euler angles was used to evaluate the best fit into the density.
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--Rigid body

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2002-04-01
Temperature (Kelvin)	93
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1100
Maximum Defocus (nm)	4400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
Calibrated Magnification	51000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	CTFFIND	3
MODEL FITTING	Insight II
MODEL FITTING	Mod-EM
MODEL FITTING	MODPIPE
MODEL FITTING	O
MODEL FITTING	RSRef
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF correction using phase flipping and setsf in EMAN to correct the amplitudes