6O96
Dot1L bound to the H2BK120 Ubiquitinated nucleosome
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 21.597 |
| f_angle_d | 0.966 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.008 |
| Sample |
|---|
| 3.5 angstroms Dot1L-H2BK120Ub Sample 1A |
| Sample Components |
| Ubiquitinated Nucleosome |
| Histone-lysine N-methyltransferase H3 lysine-79 specific |
| Ubiquitin |
| Histone octamer |
| DNA 146-MER |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | PROPANE |
| Sample Vitrification Details | blotted for 3s before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 211279 |
| Reported Resolution (Å) | 3.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1NW3, 1UBQ, 3TU4) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | 91.61 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1700 |
| Maximum Defocus (nm) | 3200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Scipion | |
| CTF CORRECTION | Gctf | v1 |
| MODEL FITTING | UCSF Chimera | 1.13.1 |
| CLASSIFICATION | RELION | |
| RECONSTRUCTION | cisTEM | |
| MODEL REFINEMENT | PHENIX | 1.14 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
