4V7H | pdb_00004v7h

Structure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution


ELECTRON MICROSCOPY
Sample
Thermomyces lanuginosus ribosome
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification DetailsApply sample, wait 30s, blot for 6s, plunge in liquid ethane
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles102689
Reported Resolution (Å)8.9
Resolution Method
Other DetailsSPIDER package. Residue H LYS 32 and Residue H VAL 33 are not properly linked. Distance of C-N bond is 2.59 Angstrom. Residue T LYS 78 and Residue T L ...SPIDER package. Residue H LYS 32 and Residue H VAL 33 are not properly linked. Distance of C-N bond is 2.59 Angstrom. Residue T LYS 78 and Residue T LEU 79 are not properly linked. Distance of C-N bond is 2.49 Angstrom.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation
Overall B Value
Fitting Procedure
DetailsMETHOD--Flexible fitting
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2005-07-07
Temperature (Kelvin)84
Microscope ModelFEI TECNAI F30
Minimum Defocus (nm)1400
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification39000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGYup.scx
RECONSTRUCTIONSPIDER