6EH1
Sacbrood virus of honeybee - expansion state II
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 27.691 |
| r_dihedral_angle_3_deg | 11.556 |
| r_dihedral_angle_4_deg | 8.07 |
| r_dihedral_angle_1_deg | 5.522 |
| r_angle_refined_deg | 0.911 |
| r_angle_other_deg | 0.592 |
| r_chiral_restr | 0.036 |
| r_bond_refined_d | 0.004 |
| r_gen_planes_refined | 0.002 |
| r_bond_other_d | 0.001 |
| Sample |
|---|
| Sacbrood virus |
| 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 | 5330 |
| Reported Resolution (Å) | 7.25 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | R-factor | ||||
| Overall B Value | 268.71 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 21 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 4000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 75000 |
| Calibrated Magnification | 74325 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminar grid screening was performed manually on FEI Tecnai F20 (cryo stage). |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| FINAL EULER ASSIGNMENT | RELION | 2 |
| CLASSIFICATION | RELION | 2 |
| RECONSTRUCTION | RELION | 2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 51000 | Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were further processed separately. Full particles classified in two types - expansion state I and II. | ||
