7UX9
Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6UXW | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 25.356 |
| f_angle_d | 0.759 |
| f_chiral_restr | 0.045 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.004 |
| Sample |
|---|
| Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) |
| Sample Components |
| DDM1 |
| Nucleosome core particle |
| Histone octamer |
| DNA double helix |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blotted for 2.5 seconds before plunging. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 215066 |
| 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 (6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 57.8 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 71.2 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2200 |
| 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 | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Warp | 1.0.9 |
| IMAGE ACQUISITION | EPU | 2.10.0.5 |
| CTF CORRECTION | Warp | 1.0.9 |
| MODEL FITTING | Coot | 0.9.2-pre |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158-000 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.0.2+210831 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.0.2+210831 |
| CLASSIFICATION | cryoSPARC | 3.0.2+210831 |
| RECONSTRUCTION | cryoSPARC | 3.0.2+210831 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | 3788872 | |||
