5ME0 | pdb_00005me0

Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YBB
experimental model	PDB	3JCN
experimental model	PDB	1HR0
experimental model	PDB	2IFE
experimental model	PDB	1TIF

Sample
30S Pre-Initiation Complex Stalled by GE81112

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	23112
Reported Resolution (Å)	13.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4YBB, 3JCN, 3JCN, 1HR0, 2IFE, 1TIF)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodie ...	The fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodies. Due to the low resolution of the volume, the conformation of the linking bases was not minimized. In addition, some of the clashes of the model are produced by flexible loops or protein side chains that were not refined.

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	17

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL 2200FSC
Minimum Defocus (nm)
Maximum Defocus (nm)
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	74183
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	1.4
IMAGE ACQUISITION	DigitalMicrograph
CTF CORRECTION	CTFFIND	4
MODEL FITTING	Situs
INITIAL EULER ASSIGNMENT	RELION	1.4
FINAL EULER ASSIGNMENT	RELION	1.4
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	Coot	0.8.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		174142

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.