2OB7

Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P6V 
Sample
Pre-accommodated ribosomal trans-translation complex: T. thermophilus 70S-mRNA-(P-site tRNA)-tmRNA-(SmpB)2-(EF-Tu)-GDP-kirromycin
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification DetailsBlot for 5 seconds before plunging. Rapid plunge freezing in liquid ethane.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles52829
Reported Resolution (Å)13.6
Resolution Method
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1P6V)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--manual fitting using stereo visualization REFINEMENT PROTOCOL--Manual
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment2004-06-01
Temperature (Kelvin)296
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1475
Maximum Defocus (nm)3635
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification55000
Calibrated Magnification49000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGO
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
CTF correction of each defocus group reconstruction, by Wiener filtering