3J81 | pdb_00003j81

CryoEM structure of a partial yeast 48S preinitiation complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U5B
experimental model	PDB	3U5C
experimental model	PDB	3V11

Sample
Partial yeast 48S preinitiation complex
Sample Components
Ribosome small subunit
Eukaryotic initiation factor 1
Eukaryotic initiation factor 1A
Eukaryotic initiation factor 2
Initiator transfer RNA
Messenger RNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	29698
Reported Resolution (Å)	4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The local resolution for chains k and l (lower-case chain IDs) is worse than the rest of the map. Therefore, these chains were docked as a rigid body ...	The local resolution for chains k and l (lower-case chain IDs) is worse than the rest of the map. Therefore, these chains were docked as a rigid body into an 8 Angstrom-resolution low-pass filtered map and then edited to remove clashes. The quality of this portion of the model is to be considered lower than the rest of the model.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3U5B, 3U5C, 3V11)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	R-factor, FSC
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	28

Imaging Experiment	1
Date of Experiment	2013-10-28
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	1600
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	78000
Calibrated Magnification	104478
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Complete dataset was collected in 5 non-consecutive days

EM Software
Task	Software Package	Version
MODEL FITTING	REFMAC
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	RELION

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