☰ Navigation Tabs
Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for differential binding of hnRNP Splicing Auxiliary Factors
SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion 1 Scattering Type neutron Radiation/Neutron Source APS BioCat 18ID beam line Synchrotron Y Beamline Type APS Detector Type Detector Manufacturer Details Temperature (K) 298 pH 6.2 Numer of Time Frames Used Protein Concentration Range (mg/mL) 6-6.5 Sample Buffer 20 mM Bis-Tris, 20 mM NaCl, pH 6.2 Data Reduction Software GNOM Guiner Mean Radius Of Gyration (nm) 2.1 Sigma Mean Radius Of Gyration 0.1 R(XS-1) Mean Cross Sectional Radii (nm) R(XS-1) Sigma Mean Cross Sectional Radii R(XS-2) Mean Cross Sectional Radii (nm) R(XS-2) Sigma Mean Cross Sectional Radii P(R) Protein Length (nm) 6.9
Solution Scattering Data Analysis and Model Fitting Method Software Software Authors Starting Model Conformers, Number Calculated Conformers, Number Submitted Conformers, Selection Criteria Best Representative Conformer Other Details NMR, SAXS NMRpipe, NMRViewJ ,X-PLOR_NIH, AMBER, GNOM Frank Delaglio; Ad Bax; Bruce Johnson; Charles Schwieters; Marius Clore; David Case; Dmitry Svergun 1024 10 Lowest energy 10
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 400 uM ESS2p 90% H2O/10% D2O 5 mM 6.5 1 atm 283 Bruker AVANCE NEO 700 2 2D 1H-13C HMQC 400 uM [U-100% 13C; U-100% 15N on ATP and GTP ESS2p 100% D2O 5 mM 6.5 1 atm 298 Bruker AVANCE II 900 3 2D 1H-1H NOESY 450 uM selective deuteration ESS2p 100% D2O 5 mM 6.5 1 atm 298 Bruker AVANCE II 800 4 2D 1H-1H TOCSY 400 uM ESS2p 90% H2O/10% D2O 5 mM 6.5 1 atm 298 Bruker AVANCE II 800 5 2D 1H-15N HSQC 300 uM Uniform_15N on GTP and UTP ESS2p 90% H2O/10% D2O 5 mM 6.5 1 atm 283 Bruker AVANCE II 800 6 2D 1H-15N HNN-COSY 300 uM Uniform_15N on all nucleotides ESS2p 90% H2O/10% D2O 5 mM 6.5 1 atm 283 Bruker AVANCE II 900
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE II 900 2 Bruker AVANCE II 800 3 Bruker AVANCE NEO 700
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 1024 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman 2 structure calculation X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 3 chemical shift assignment NMRViewJ Bruce Johnson 4 collection TopSpin Bruker Biospin 5 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 6 data analysis NMRFAM-SPARKY Woonghee Lee, Marco Tonelli, John L Markley