7SJ8
13pf wildtype microtubule from recombinant human tubulin decorated with kinesin
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6DPU | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 14.311 |
| f_angle_d | 0.563 |
| f_chiral_restr | 0.042 |
| f_bond_d | 0.005 |
| f_plane_restr | 0.004 |
| Sample |
|---|
| 13pf wildtype microtubule from recombinant human tubulin and decorated with kinesin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | 30 second adsorption time onto grid. blot force 15, 4 second blot time, 37 degrees, and 100 percent humidity. 0.5 second drain time. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 23364 |
| Reported Resolution (Å) | 3.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 81.69 |
| Angular Rotation | -0.09 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6DPU) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation Coefficient | ||||
| Overall B Value | 115 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 2400 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.6 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 64000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 4 |
| CTF CORRECTION | RELION | 3.1 |
| MODEL FITTING | PHENIX | dev-2883 |
| MODEL REFINEMENT | PHENIX | dev-2883 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.11 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | FREALIGN | 9.11 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTFFind4 and CTFRefine were used within the RELION3.1 framework. | Microtubules were picked within RELION 3.1 helical picking functionality and extracted along the filament with an 82A sliding box. | ||
