RNA polymerase II initially transcribing complex with a 6-nt RNA and the +1 nucleosome
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 17.5755 |
| f_angle_d | 1.1998 |
| f_chiral_restr | 0.0653 |
| f_plane_restr | 0.0123 |
| f_bond_d | 0.006 |
| Sample |
|---|
| RNA polymerase II initially transcribing complex with a 6-nt RNA and the +1 nucleosome |
| Sample Components |
| General transcription factor IIH |
| Mammalian RNA polymerase II |
| Nucleosome (protein) |
| Nucleosome (DNA) |
| General transcription factor IIB |
| TATA-box binding protein (TBP) |
| 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 | 40410 |
| Reported Resolution (Å) | 7.6 |
| 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) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 1500 |
| 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 ChimeraX | 1.9 |
| MODEL REFINEMENT | ISOLDE | 1.9 |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| FINAL EULER ASSIGNMENT | RELION | 5.0 |
| RECONSTRUCTION | RELION | 5.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 10038896 | |||
