Structure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.484 |
| f_angle_d | 0.451 |
| f_chiral_restr | 0.041 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| Autographa californica multiple nucleopolyhedrovirus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grid was blotted using zero incubation time, blot time of 2 s, blot force of -10 and drain time of 1 s. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1002951 |
| Reported Resolution (Å) | 3.06 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final reconstruction was generated using local refinement in cryoSPARC. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | ChimeraX was used to perform rigid-body fitting of an AlphaFold2 model. Flexible modeling was performed using Coot and refined in Phenix. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 47.3 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 1200 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.1.2 |
| PARTICLE SELECTION | EMAN2 | 2.2 |
| PARTICLE SELECTION | RELION | 2.1 |
| IMAGE ACQUISITION | EPU | 1 |
| CTF CORRECTION | cryoSPARC | 4.1.2 |
| MODEL FITTING | UCSF ChimeraX | 1.5 |
| MODEL FITTING | Coot | 0.9.8.6 |
| MODEL REFINEMENT | PHENIX | 1.20.1_4487 |
| INITIAL EULER ASSIGNMENT | SPRING | 0.84.1470 |
| INITIAL EULER ASSIGNMENT | RELION | 2.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.1.2 |
| CLASSIFICATION | cryoSPARC | 4.1.2 |
| RECONSTRUCTION | cryoSPARC | 4.1.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction | 2165694 | Manually selected particles in EMAN2 were used to create a 2D template in cryoSPARC for automated filament tracing resulting in 77,356 particles. After helical refinement and symmetry expansion, 2,165,694 subparticles were extracted. | |
