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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