HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL
ELECTRON MICROSCOPY - SOLUTION NMR
NMR Experiment |
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
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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 |
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Spectrometer | Manufacturer | Model | Field Strength |
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1 | Bruker | AVANCE | 600 |
NMR Refinement |
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Method | Details | Software |
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molecular dynamics | Used GB for solvent simulation, NOEs and EM data simultaneously as restraints | Amber |
NMR Ensemble Information |
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Conformer Selection Criteria | all calculated structures submitted |
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Conformers Calculated Total Number | 20 |
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Conformers Submitted Total Number | 20 |
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Representative Model | 1 (lowest energy) |
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Additional NMR Experimental Information |
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Details | NMR studies conducted with multiple samples prepared by differential nucleotide-specific 2H labeling. |
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Computation: NMR Software |
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# | Classification | Version | Software Name | Author |
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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 |
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Human immunodeficiency virus 1 |
Specimen Preparation |
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Sample Aggregation State | PARTICLE |
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Vitrification Instrument | FEI VITROBOT MARK IV |
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Cryogen Name | ETHANE |
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Sample Vitrification Details | |
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3D Reconstruction |
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Reconstruction Method | SUBTOMOGRAM AVERAGING |
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Number of Particles | 20366 |
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Reported Resolution (Å) | 9 |
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Resolution Method | FSC 0.143 CUT-OFF |
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Other Details | |
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Refinement Type | |
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Symmetry Type | POINT |
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Point Symmetry | C2 |
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Data Acquisition |
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Detector Type | DIRECT ELECTRON DE-12 (4k x 3k) |
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Electron Dose (electrons/Å**2) | 75 |
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Imaging Experiment | 1 |
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Date of Experiment | |
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Temperature (Kelvin) | |
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Microscope Model | JEOL 2200FS |
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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 | |
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Imaging Mode | BRIGHT FIELD |
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Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
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Nominal Magnification | 25000 |
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Calibrated Magnification | |
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Source | FIELD EMISSION GUN |
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Acceleration Voltage (kV) | 200 |
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Imaging Details | |
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EM Software |
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Task | Software Package | Version |
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VOLUME SELECTION | EMAN2 | 2.1 |
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CTF CORRECTION | EMAN2 | 2.1 |
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RECONSTRUCTION | EMAN2 | 2.1 |
Image Processing |
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details |
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PHASE FLIPPING AND AMPLITUDE CORRECTION | | | |