ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| in silico model | AlphaFold | ||
| experimental model | PDB | 3TU4 | |
| experimental model | PDB | 8H1T | |
| experimental model | PDB | 8SVF | |
| experimental model | PDB | 4R8P | |
| experimental model | PDB | 2D9G | |
| in silico model | SwissModel | ||
| experimental model | PDB | 1UBQ | |
| experimental model | PDB | 7PFV | |
| Sample |
|---|
| ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome |
| Sample Components |
| Histones |
| DNA |
| ncPRC1-RYBP |
| Ubiquitin |
| Histone H3.2 |
| Histone H4 |
| Histone H2A |
| Histone H2B 1.1 |
| DNA (187-MER) |
| DNA (187-MER) |
| Polycomb complex protein BMI-1 |
| E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 |
| RING1 and YY1-binding protein |
| Histone H1.4 |
| 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 | 205635 |
| Reported Resolution (Å) | 3.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3tu4, 8H1T, 8SVF, 4R8P, 2D9G, 1UBQ, 7PFV) | 2 (2WWZ) | |||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 61.06 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Leginon | v 3.6 |
| MODEL FITTING | UCSF ChimeraX | 1.7.1 |
| MODEL FITTING | Coot | 0.9.8.94 |
| RECONSTRUCTION | cryoSPARC | 4.4 |
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1394967 | |||
