Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1Y1V | |
| Sample |
|---|
| RNA polymerase II VP16-Mediator-pol II-TFIIF assembly |
| Sample Components |
| core Mediator |
| RNA polymerase II |
| TFIIF |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| Staining Type | NEGATIVE |
| Staining Material | ammonium molybdate |
| Staining Details | grids with adsorbed protein washed 3x with buffer containing 5% trehalose, 20 mM HEPES, 100 mM KCl, and 0.10 mM EDTA, then subjected to cryo-negative ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 3146 |
| Reported Resolution (Å) | 36 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | The particles were selected interactively. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1Y1V) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | contour-based Laplacian correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--rigid body DETAILS--the TFIIS chain S was removed before fitting | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 15 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TECNAI F20 |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 4500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN LIQUID NITROGEN |
| Nominal Magnification | 29000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Situs | |
| RECONSTRUCTION | SPIDER | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| each micrograph | ||||
