5OXE
Structure of major capsid protein VP1 of Aeropyrum pernix bacilliform virus 1 APBV1
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.726 |
| r_dihedral_angle_3_deg | 24.644 |
| r_long_range_B_refined | 22.829 |
| r_long_range_B_other | 22.828 |
| r_scangle_other | 19.055 |
| r_dihedral_angle_4_deg | 15.731 |
| r_mcangle_it | 13.873 |
| r_mcangle_other | 13.872 |
| r_scbond_it | 11.654 |
| r_scbond_other | 11.65 |
| Sample |
|---|
| Aeropyrum pernix bacilliform virus 1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 94645 |
| Reported Resolution (Å) | 3.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C5 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| 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 | |
| Nominal Magnification | |
| Calibrated Magnification | 37037 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 3 |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | SPRING | |
| FINAL EULER ASSIGNMENT | SPRING | |
| RECONSTRUCTION | SPRING | |
| MODEL REFINEMENT | REFMAC | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 169316 | Overlapping segments extracted from helical particles | ||
