HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL
ELECTRON MICROSCOPY - SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY (2H-EDITED) | 400 uM Fully protonated, 5 mM NaCl, 140 mM KCl, 1 mM MgCl2, Tris | 100% D2O | 150 mM | 7.1 | 1 atm | 308 | Bruker AVANCE 600 |
| 2 | ABUNDANCE 13C-1H HMQC | 400 uM Fully protonated, 5 mM NaCl, 140 mM KCl, 1 mM MgCl2, Tris | 100% D2O | 150 mM | 7.1 | 1 atm | 308 | Bruker AVANCE 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | Used GB for solvent simulation, NOEs and EM data simultaneously as restraints | Amber |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 20 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | NMR studies conducted with multiple samples prepared by differential nucleotide-specific 2H labeling. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 3 | processing | NMRFx | Bruce Johnson, One Moon Scientific | |
| 4 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 5 | structure calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
| 6 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 8 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 9 | peak picking | NMRView | Johnson, One Moon Scientific | |
| Sample |
|---|
| Human immunodeficiency virus 1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 20366 |
| Reported Resolution (Å) | 9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | DIRECT ELECTRON DE-12 (4k x 3k) | ||||||||
| Electron Dose (electrons/Å**2) | 75 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL 2200FS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
| Nominal Magnification | 25000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | EMAN2 | 2.1 |
| CTF CORRECTION | EMAN2 | 2.1 |
| RECONSTRUCTION | EMAN2 | 2.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
