CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109
ELECTRON MICROSCOPY
| Sample |
|---|
| HCMV Trimer gHgLgO bound to human receptor PDGFRa and neutralizing fabs 13H11 and MSL-109 |
| Sample Components |
| HCMV Trimer gHgLgO |
| PDGFRa and neutralizing fabs 13H11 and MSL-109 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 2D ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 2.5 seconds before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 3560620 |
| Reported Resolution (Å) | 2.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Used score threshold of 0.25 for final 3D reconstruction. Map used for model refinements is a composite map after combining 3 focussed maps with PHENI ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| 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 | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Gautomatch | 0.56 |
| IMAGE ACQUISITION | SerialEM | 3.7.11 |
| CTF CORRECTION | CTFFIND | |
| MODEL FITTING | UCSF Chimera | 1.13.1 |
| MODEL FITTING | Coot | 0.8.9 |
| MODEL REFINEMENT | PHENIX | 1.19 |
| MODEL REFINEMENT | ISOLDE | 1.1.0 |
| INITIAL EULER ASSIGNMENT | cisTEM | 1.02 |
| FINAL EULER ASSIGNMENT | cisTEM | 1.02 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | cisTEM | 1.02 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 4151085 | |||
