6VCC
Cryo-EM structure of the Dvl2 DIX filament
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6IW3 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.767 |
| f_angle_d | 0.619 |
| f_chiral_restr | 0.054 |
| f_plane_restr | 0.006 |
| f_bond_d | 0.003 |
| Sample |
|---|
| Segment polarity protein dishevelled homolog DVL-2 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | The grid was blotted for 2.0 s using Whatman #1 filter paper (GE Healthcare). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 110105 |
| Reported Resolution (Å) | 3.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 13.5 |
| Angular Rotation | 48 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6IW3) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The two mutations in the source (Y27W and C80S) were reverted to Trp and Ser, respectively, before fitting. Model refinement was carried out through ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 98 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| 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 | |
| Calibrated Magnification | 29000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| IMAGE ACQUISITION | DigitalMicrograph | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | PHENIX | 1.17.1-3660 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.8 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.8 |
| CLASSIFICATION | RELION | 3.0.8 |
| RECONSTRUCTION | RELION | 3.0.8 |
| MODEL REFINEMENT | PHENIX | 1.17.1-3360 |
| MODEL REFINEMENT | Coot | 0.8.9.2 EL |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 437872 | |||
