7M1X
Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 24.338 |
| f_angle_d | 0.757 |
| f_chiral_restr | 0.042 |
| f_plane_restr | 0.022 |
| f_bond_d | 0.007 |
| Sample |
|---|
| Nucleosome core particle containing variant H2A.Z and canonical core histones |
| Sample Components |
| Histone H3 |
| Histone H4 |
| Histone variant H2A.Z |
| Histone H2B |
| DNA (136-MER) |
| DNA (136-MER) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 4.5 seconds before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 42826 |
| Reported Resolution (Å) | 3.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1F66, 1F66, 1F66, 1F66, 1F66, 1F66, 1F66, 1F66, 6FQ5, 6FQ5) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | rmsd | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 33 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2500 |
| 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 | 92000 |
| Calibrated Magnification | 123811 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1.14 |
| MODEL FITTING | RELION | 3.1.0 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.1.0 |
| CLASSIFICATION | RELION | 3.1.0 |
| RECONSTRUCTION | RELION | 3.1.0 |
| 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 | 127778 | |||
