Structure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab at a nominal resolution of 4.6 Angstrom
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 7.1 |
| f_angle_d | 0.744 |
| f_chiral_restr | 0.071 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| HIV-1 GP160 trimer:PG16 Fab complex |
| Sample Components |
| HIV envelope glycoprotein GP160 (mature) |
| Antibody PG16 Fab |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 4.2 second blot before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 492995 |
| Reported Resolution (Å) | 4.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| 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 | 300 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.26 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 29000 |
| Calibrated Magnification | 30488 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | 3.5.6 |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | UCSF Chimera | 1.13.1 |
| MODEL REFINEMENT | PHENIX | 14 |
| INITIAL EULER ASSIGNMENT | RELION | 2.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.4 |
| CLASSIFICATION | RELION | 3.0.4 |
| RECONSTRUCTION | RELION | 3.0.4 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
