5LZC
Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the codon reading state (CR)
ELECTRON MICROSCOPY
Sample |
---|
Codon reading state of E. coli ribosome 70S-SelB-GDPNP-Sec-tRNASec-fMet-tRNAfmet-SECIS mRNA complex (CR) |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 11658 |
Reported Resolution (Å) | 4.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Gold-standard refinement of independent half maps in Relion 1.3 |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | |||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Maximum likelihood | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | For parts of the model exhibiting larger conformational differences and/or lower local map resolution, additional cycles of real space refinement and ... |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 30 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 700 |
Maximum Defocus (nm) | 2600 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 0.001 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 59000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Using a Cs-corrector from CEOS electron optical aberrations were corrected to residual phase errors of 45degree at scattering angles of >12 to 15 mrad. |
EM Software | ||
---|---|---|
Task | Software Package | Version |
MODEL REFINEMENT | Rosetta | 3.5 |
MODEL REFINEMENT | Coot | 0.8.3 |
MODEL REFINEMENT | RCrane | 1.1 |
MODEL REFINEMENT | PHENIX | 1.10.1 & developmental |
MODEL REFINEMENT | PHENIX | 1.10.1 |
RECONSTRUCTION | RELION | 1.3 |
MODEL REFINEMENT | ERRASER |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | Local CTF correction, after MSA based classification and averaging of local power spectra | 969526 | 969526 ribosome particles showing Thon rings better than 3.5A (see CTF correction) |