6USJ
Structure of two nucleosomes bridged by human PARP2
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 26.8363 |
| f_angle_d | 1.9379 |
| f_chiral_restr | 0.0942 |
| f_plane_restr | 0.0203 |
| f_bond_d | 0.0148 |
| Sample |
|---|
| Two nucleosomes bridged by PARP2 |
| Sample Components |
| histone |
| DNA |
| PARP2 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot time 2s, blot force 0 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 27889 |
| Reported Resolution (Å) | 10.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6F5B, 6F5B, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 6R1T, 6R1T) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Real-space CC | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 56.1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TECNAI F30 |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | UCSF Chimera | 1.13.1 |
| MODEL REFINEMENT | PHENIX | 1.17-3644 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.0 |
| CLASSIFICATION | RELION | 3.0 |
| RECONSTRUCTION | RELION | 3.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 226250 | Picked using crYOLO version 1.3.1 with a model trained on the same dataset (with the generic model provided with crYOLO used as pre-trained weights). | ||
