5UK2
CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 4
ELECTRON MICROSCOPY
| Sample |
|---|
| Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 142314 |
| Reported Resolution (Å) | 4.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Refinement and classification were limited to 10 Angstrom resolution. |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Domains were initially placed manually using Chimera. The HA trimer was from PDB ID 5UGY. Fab was initially obtained using MODELLER, with PDB ID 4K8R ... | ||||
| 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 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 | 18000 |
| Calibrated Magnification | 30444 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND3 | |
| MODEL FITTING | Manual placement | |
| INITIAL EULER ASSIGNMENT | IMAGIC | |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.11 |
| CLASSIFICATION | FREALIGN | 9.11 |
| RECONSTRUCTION | FREALIGN | 9.11 |
| MODEL REFINEMENT | PHENIX | 1.10_2155 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 252130 | |||
