3IYQ | pdb_00003iyq

tmRNA-SmpB: a journey to the center of the bacterial ribosome

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CZJ
experimental model	PDB	2OB7

Sample
Thermus thermophilus 70S ribosome

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	49061
Reported Resolution (Å)	13
Resolution Method	FSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2CZJ)	2 (2OB7)
Refinement Space	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target	Cross-Correlation	Cross-Correlation
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--Rigid Body and flexible fitting DETAILS--The domains were initially separately fitted by manual docking and then further optimized using mdff.	REFINEMENT PROTOCOL--Rigid Body and flexible fitting DETAILS--each subdomain (H2b-c, H5, pk1, pk2, pk3, pk4) were initially separately fitted by manual docking and then further optimized using mdff.

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

Imaging Experiment	1
Date of Experiment	2009-07-01
Temperature (Kelvin)	95
Microscope Model	JEOL 2200FS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2200
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	45700
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

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

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