4V6S
Structural characterization of mRNA-tRNA translocation intermediates (class 3 of the six classes)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2I2V | |
| Sample |
|---|
| Trp-tRNA-EFTu-GDP-kir-70S ribosome |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | NITROGEN |
| Sample Vitrification Details | Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 21000 |
| Reported Resolution (Å) | 13.1 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2I2V) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | RMSD, cross correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--Molecular Dynamics based flexible fitting | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TVIPS TEMCAM-F415 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2011-05-01 |
| Temperature (Kelvin) | 80.7 |
| Microscope Model | FEI TECNAI F30 |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 4000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.26 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 59000 |
| Calibrated Magnification | 58269 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | automated data collection system AutoEMation (CCD mag. 100000x) |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | MDFF | |
| RECONSTRUCTION | SPIDER | |
| RECONSTRUCTION | Xmipp | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| Volumes were CTF-corrected in defocus groups | ||||
