7K01
Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex
ELECTRON MICROSCOPY
| Sample |
|---|
| Ternary complex of TFIIH/Rad4-Rad23-Rad33 with AAF damaged DNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM CPC |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grids were manually blotted for 2-3 seconds prior to plunge freezing |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 56101 |
| Reported Resolution (Å) | 3.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final reconstruction performed in RELION. Map locally filtered to FSC=0.5 by blocres |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5OQJ, 6NMI) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2800 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Images collected with image shift |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 4.13 |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | PHENIX | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.8 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.8 |
| RECONSTRUCTION | RELION | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1159858 | Particles picked by elliptical blob picking in cryoSPARC | ||
