8BYQ
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
ELECTRON MICROSCOPY
| Sample |
|---|
| RNA polymerase II pre-initiation complex with the proximal +1 nucleosome |
| Sample Components |
| General transcription factor IIH |
| Mammalian RNA polymerase II |
| Nucleosome (protein) |
| Nucleosome (DNA) |
| General transcription factor IIB |
| TATA-box binding protein |
| General transcription factor IIF |
| General transcription factor IIA |
| General transcription factor IIE |
| 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 | 101994 |
| Reported Resolution (Å) | 4.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.45 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 1300 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Warp | 1.0.9 |
| IMAGE ACQUISITION | SerialEM | 4.0 |
| CTF CORRECTION | Warp | 1.0.9 |
| MODEL FITTING | UCSF Chimera | |
| MODEL REFINEMENT | ISOLDE | 1.3 |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 4606320 | |||
