6FTX
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_scangle_other | 67.234 |
| r_mcangle_it | 60.148 |
| r_mcangle_other | 60.145 |
| r_scbond_other | 43.08 |
| r_scbond_it | 43.077 |
| r_mcbond_other | 37.444 |
| r_mcbond_it | 37.441 |
| r_dihedral_angle_2_deg | 32.729 |
| r_dihedral_angle_1_deg | 22.261 |
| r_dihedral_angle_4_deg | 20.549 |
| Sample |
|---|
| X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
| Sample Components |
| X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
| X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
| X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
| X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 135000 |
| Reported Resolution (Å) | 4.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 204 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 4000 |
| 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 | 35714 |
| Calibrated Magnification | 35714 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | CCP4 package | |
| INITIAL EULER ASSIGNMENT | RELION | |
| FINAL EULER ASSIGNMENT | RELION | |
| CLASSIFICATION | RELION | |
| RECONSTRUCTION | RELION | |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 860000 | |||
