5GJE
Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1
ELECTRON MICROSCOPY
| Sample |
|---|
| Human LRP6 ectodomain complexed with full length of Dkk1 |
| Sample Components |
| LRP6 ectodomain |
| Human Dickkopf-related protein1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Staining Type | NONE |
| Staining Material | Uranyl acetate |
| Staining Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 5390 |
| Reported Resolution (Å) | 21 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4DG6, 3S2K, 3S2K) | ||||
| Refinement Space | |||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TVIPS TEMCAM-F224 (2k x 2k) | ||||||||
| Electron Dose (electrons/Å**2) | 20 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | HITACHI H-9500SD |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.8 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | SIDE ENTRY, EUCENTRIC |
| Nominal Magnification | 80000 |
| Calibrated Magnification | |
| Source | LAB6 |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | SPIDER & WEB | 17 |
| IMAGE ACQUISITION | EM-Menu | 4 |
| CTF CORRECTION | SPIDER | |
| MODEL FITTING | Chimera | 1.10.1 |
| INITIAL EULER ASSIGNMENT | SPIDER | |
| FINAL EULER ASSIGNMENT | SPIDER | |
| CLASSIFICATION | SPIDER | |
| RECONSTRUCTION | SPIDER | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | This was not done for RCT but for following single-particle reconstruction | 10974 tilt pairs for RCT | ||
