Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| in silico model | AlphaFold | Q57YA3 | |
| experimental model | PDB | 8COM | |
| in silico model | AlphaFold | Q389T1 | |
| in silico model | AlphaFold | Q387X7 | |
| in silico model | AlphaFold | Q587H6 | |
| in silico model | AlphaFold | ||
| Sample |
|---|
| H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei reconstituted with Widom 601 145 bp DNA |
| Sample Components |
| Histone octamer |
| Widom 601 145 bp DNA |
| 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 | 362400 |
| Reported Resolution (Å) | 3.21 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8COM) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | 116 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 54.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 3300 |
| 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 | 83000 |
| Calibrated Magnification | 83000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.6.2 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 4.6.2 |
| MODEL FITTING | UCSF ChimeraX | 1.7.1 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.6.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.6.2 |
| CLASSIFICATION | cryoSPARC | 4.6.2 |
| RECONSTRUCTION | cryoSPARC | 4.6.2 |
| MODEL REFINEMENT | PHENIX | 1.21.1 |
| MODEL REFINEMENT | Coot | 0.9.8.7 |
| MODEL REFINEMENT | ISOLDE | 1.7.1 |
| MODEL REFINEMENT | UCSF ChimeraX | 1.7.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 5780374 | |||
