8VJR
Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 9-14-18, DTT-treated
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8VG6 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.5297 |
| f_angle_d | 1.3982 |
| f_chiral_restr | 0.0884 |
| f_bond_d | 0.0143 |
| f_plane_restr | 0.0069 |
| Sample |
|---|
| Tulane virus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | GATAN CRYOPLUNGE 3 |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 44239 |
| Reported Resolution (Å) | 2.63 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8VG6) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 23 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Leginon | |
| MODEL FITTING | PHENIX | |
| MODEL FITTING | Coot | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | UCSF ChimeraX | |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | Rosetta | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | |
| FINAL EULER ASSIGNMENT | cryoSPARC | |
| FINAL EULER ASSIGNMENT | jspr | |
| CLASSIFICATION | cryoSPARC | |
| RECONSTRUCTION | jspr | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
