Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus.
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1THD | |
| Sample |
|---|
| Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 2885 |
| Reported Resolution (Å) | 24 |
| Resolution Method | |
| Other Details | THE COORDINATES IN THIS ENTRY CONTAIN CA ONLY |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1THD) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Using EMFIT | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--place coordinates manually and then optimise position using program REFINEMENT PROTOCOL--rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 2.39 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2007-03-21 |
| Temperature (Kelvin) | 87 |
| Microscope Model | FEI/PHILIPS CM200T |
| Minimum Defocus (nm) | 2276 |
| Maximum Defocus (nm) | 3373 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 50000 |
| Calibrated Magnification | 51040 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details | low dose |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | EMfit | |
| RECONSTRUCTION | SPIDER | |
| RECONSTRUCTION | Xmipp | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| phase flip | ||||
