3J6X
S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II)
ELECTRON MICROSCOPY
| Sample |
|---|
| ribosome-IRES complex |
| Sample Components |
| 80S Ribosome |
| Internal Ribosome Entry Site |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 52444 |
| Reported Resolution (Å) | 6.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | (Single particle--Applied symmetry: C1) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3U5B, 3U5C, 3U5D, 3U5E) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--rigid body DETAILS--(1) TSV IRES was modeled with iFoldRNA and ModeRNA programs and then fitted into the cryo-EM map in Chimera. ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON I (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 30 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2012-12-26 |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1150 |
| Maximum Defocus (nm) | 6530 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.01 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 133333 |
| Calibrated Magnification | 132138 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | CTFFIND | 3 |
| MODEL FITTING | CNS | |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | EMAN | 2 |
| RECONSTRUCTION | FREALIGN | |
| RECONSTRUCTION | IMAGIC | |
| RECONSTRUCTION | RSAMPLE | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| CTFFIND3, FREALIGN per micrograph | ||||
