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) | |
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| Maximum Defocus (nm) | |
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| Minimum Tilt Angle (degrees) | |
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| Maximum Tilt Angle (degrees) | |
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| 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 |
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| CTF CORRECTION | EMAN2 | 2.1 |
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| RECONSTRUCTION | EMAN2 | 2.1 |
| Image Processing |
|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details |
|---|
| PHASE FLIPPING AND AMPLITUDE CORRECTION | | | |
