3JD6
Double octamer structure of retinoschisin, a cell-cell adhesion protein of the retina
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1SDD | |
| Sample |
|---|
| Purified Retinoschisin: residues 24-224 + 6xHis |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Ambient temperature 23 degrees C. Plunged into liquid ethane (LEICA EM GP). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 9096 |
| Reported Resolution (Å) | 4.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D8 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1SDD) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | FSC(0.5) = 4.7 | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--Flexible fitting REFINEMENT PROTOCOL--FLEXIBLE | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 30 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2014-06-03 |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 39000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | 10 frames over 3 seconds |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Coot | |
| MODEL FITTING | Foldit | |
| MODEL FITTING | MDFF | |
| RECONSTRUCTION | EMAN | 2 |
| RECONSTRUCTION | RELION | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| Included in iterative refinement | ||||
