Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide (Apo state 2)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3VKG | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.776 |
| f_angle_d | 0.458 |
| f_chiral_restr | 0.037 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the absence of nucleotide |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 910656 |
| Reported Resolution (Å) | 2.66 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | The selected particles were refined by non-uniform refinement in cryoSPARC. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3VKG) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Real-space target; weighted map sum at atom centers | ||||
| Overall B Value | 92.3 | ||||
| Fitting Procedure | |||||
| Details | A monomeric HF380 motor-domain model was fitted into the cryo-EM map and refined by phenix.real_space_refine. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 80 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL CRYO ARM 300 |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | JEOL CRYOSPECPORTER |
| Nominal Magnification | 60000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.4.1 |
| IMAGE ACQUISITION | SerialEM | 3.8 or 4.050 |
| CTF CORRECTION | cryoSPARC | 4.4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.7 |
| MODEL FITTING | Coot | 0.9.8.92 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.4.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.4.1 |
| CLASSIFICATION | cryoSPARC | 4.4.1 |
| RECONSTRUCTION | cryoSPARC | 4.4.1 |
| MODEL REFINEMENT | PHENIX | 1.21_5207 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF parameters were estimated using Patch CTF estimation in cryoSPARC and further refined by global and local CTF refinement. | 1108632 | Particles were selected by blob picking and template-based picking in cryoSPARC. Template-picked particles were extracted with a 300-pixel box and cleaned by 2D classification, yielding 1,108,632 particles. | |
