Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule
ELECTRON MICROSCOPY
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | hanging drop | 6.5 | 277 | 0.1 MES, 15% PEG 20000, Se-MET Derivative, pH 6.5, hanging drop, temperature 277K |
| 2 | hanging drop | 6.5 | 277 | 0.1 MES, 15% PEG 20000, NATIVE PROTEIN, pH 6.5, hanging drop, temperature 277K |
Diffraction
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9790, 0.9796, 0.9184 | NSLS | X6A |
| 2 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9791 | NSLS | X6A |
Data Collection
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 23.8 |
| c_improper_angle_d | 2.27 |
| c_angle_deg | 1.6 |
| c_bond_d | 0.006 |
| c_mcbond_it | |
| c_mcangle_it | |
| c_scbond_it | |
| c_scangle_it | |
| Sample |
|---|
| Nucleotide-Free NOD (3DC4)Complexed to Microtubule |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | |
| Reported Resolution (Å) | 11 |
| Resolution Method | |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3DC4, 1JFF) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 16 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL 4000EX |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 1500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 60000 |
| Calibrated Magnification | |
| Source | LAB6 |
| Acceleration Voltage (kV) | 400 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Situs | |
| RECONSTRUCTION | SPIDER | |
