2BCW | pdb_00002bcw

Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70S*EF-G*GDP*fusidic acid complex

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MMS
experimental model	PDB	1CTF
experimental model	PDB	1ELO

Sample
70S*EF-G*GDP*FUSIDIC ACID COMPLEX
Sample Components
50S ribosomal protein L11
50S ribosomal protein L7/L12
Elongation factor G

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details	RAPID-FREEZING IN LIQUID ETHANE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	11.2
Resolution Method
Other Details	PROJECTION MATCHING USING SPIDER PACKAGE
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1MMS, 1CTF, 1ELO)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	The X-ray crystallographic structure of the EF-G individual domains were fitted into the cryo-EM map of the 70S*EF-G-UG*GDP*Fusidic acid complex using O. The G' domain within domain I was separately fitted, using a combination of manual rigid-body docking and flexible docking approaches, and taking into consideration both the cryo-EM envelope and the positional constraints imposed by the UG density. X-ray crystallographic structures of the N-terminal domain of protein L11 and C-terminal domain of protein L7/L12 were fitted as rigid bodies.
Overall B Value
Fitting Procedure
Details	METHOD--A COMBINATION OF MANUAL RIGID-BODY DOCKING AND FLEXIBLE DOCKING REFINEMENT PROTOCOL--A COMBINATION OF MANUAL RIGID-BODY DOCKING AND FLEXIBLE DOCKING

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

Imaging Experiment	1
Date of Experiment	2004-11-09
Temperature (Kelvin)	93
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	-0.7
Maximum Defocus (nm)	-3.5
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
Calibrated Magnification	50760
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	OTHER
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF CORRECTION OF 3D MAPS BY WIENER FILTRATION