6R3B
BACTERIOPHAGE SPP1 PROCAPSID-I PROTEIN
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4AN5 | |
| Sample |
|---|
| Bacillus phage SPP1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 4558 |
| Reported Resolution (Å) | 4.5 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4AN5) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 BASE (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 900 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.3 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER |
| Nominal Magnification | 39000 |
| Calibrated Magnification | 39000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | EMAN2 | |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | IMAGIC | 5 |
| FINAL EULER ASSIGNMENT | IMAGIC | 5 |
| CLASSIFICATION | IMAGIC | 5 |
| RECONSTRUCTION | IMAGIC | 5 |
| MODEL REFINEMENT | Coot | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | Assessment of the contrast transfer function of the microscope was done using CTFFIND4 | 6078 | ||
