6C22
Capsid protein in the Staphylococcus aureus phage 80alpha-derived SaPI1 mature capsid
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 15.395 |
| r_long_range_B_refined | 5.524 |
| r_dihedral_angle_2_deg | 4.434 |
| r_dihedral_angle_1_deg | 1.714 |
| r_angle_refined_deg | 1.064 |
| r_mcangle_it | 0.829 |
| r_mcbond_it | 0.435 |
| r_scbond_it | 0.089 |
| r_chiral_restr | 0.052 |
| r_bond_refined_d | 0.006 |
| Sample |
|---|
| Staphylococcus phage 80alpha |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 6471 |
| Reported Resolution (Å) | 8.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| 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 | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TECNAI F20 |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 62000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | EMAN | 1.9 |
| CTF CORRECTION | EMAN | 1.9 |
| MODEL FITTING | UCSF Chimera | 1.10.2 |
| MODEL REFINEMENT | REFMAC | 5.8.0158 |
| MODEL REFINEMENT | Coot | 0.8.8 |
| MODEL REFINEMENT | Coot | 0.8.6.1 |
| INITIAL EULER ASSIGNMENT | Auto3DEM | 4.01 |
| FINAL EULER ASSIGNMENT | Auto3DEM | 4.01 |
| CLASSIFICATION | Auto3DEM | 4.01 |
| RECONSTRUCTION | Auto3DEM | 4.01 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | 6471 | |||
