9B3P
The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome
ELECTRON MICROSCOPY
| Sample |
|---|
| nucleosome containing histone variants H3.3 and H2A.Z |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Freezing condition: blot force 0, blot time 4.5 second |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 205792 |
| Reported Resolution (Å) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5B33, 5B33, 5B33, 5B33, 5B33, 5B33, 5B33, 5B33, 6fq5, 6fq5) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 87.42 | ||||
| Fitting Procedure | |||||
| Details | Phenix real-space refinement was used. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (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) | 1000 |
| Maximum Defocus (nm) | 2250 |
| 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 | |
| Calibrated Magnification | 81000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.5 |
| INITIAL EULER ASSIGNMENT | RELION | 4.0 |
| FINAL EULER ASSIGNMENT | RELION | 4.0 |
| CLASSIFICATION | RELION | 4.0 |
| RECONSTRUCTION | RELION | 4.0 |
| MODEL REFINEMENT | PHENIX | 1.15.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1291847 | |||
