1YXN
Pseudo-atomic model of a fiberless isometric variant of bacteriophage phi29
ELECTRON MICROSCOPY
| Sample |
|---|
| Fiberless isometric phi29 capsid |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | frozen in liquid ethane |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 5922 |
| Reported Resolution (Å) | 7.9 |
| Resolution Method | |
| Other Details | Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | rigid body refinement in real space against laplacian filtered EM density, using the program COLORES in the package SITUS. Each molecule in the T=3 asymmetric unit was refined separately. | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--6D search for each symmetry related molecule in the icosahedral asymmetric unit REFINEMENT PROTOCOL--rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 20 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | 100 |
| Microscope Model | FEI/PHILIPS CM200FEG/ST |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 38000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | EMfit | |
| MODEL FITTING | SITUS COLORES | |
| MODEL FITTING | SITUS COLORES | |
| RECONSTRUCTION | EM3DR | |
| RECONSTRUCTION | PFT | |
| RECONSTRUCTION | POR | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| Inverse of CTF was applied to images. Both phases and amplitudes were corrected. | ||||
