3JAP
Structure of a partial yeast 48S preinitiation complex in closed conformation
ELECTRON MICROSCOPY
| Sample |
|---|
| Partial yeast 48S preinitiation complex |
| Sample Components |
| 40S ribosome |
| Eukaryotic initiation factor eIF1A |
| Eukaryotic initiation factor eIF2 |
| Eukaryotic initiation factor eIF1 |
| Eukaryotic initiation factor eIF3 |
| Met-tRNAi |
| mRNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 21401 |
| Reported Resolution (Å) | 4.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | gold-standard |
| Refinement Type | HALF-MAPS REFINED INDEPENDENTLY |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3J81, 3CW2, 2D74, 4U1C, 4U1D, 4U1E) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | R-factor, FSC | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--Local refinement | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 27 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2014-07-04 |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 4000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 59000 |
| Calibrated Magnification | 104478 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Complete dataset was collected over two non-consecutive days. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Coot | |
| MODEL FITTING | REFMAC | |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | RELION | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| Each particle | ||||
