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Solution structure of the major PDGFRB promoter G-quadruplex with a broken-strand G21 fill-in
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-13C HSQC 1.06 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*G)-3'), 75 mM potassium chloride, 25 mM potassium phosphate 90% H2O/10% D2O 100 mM 7.0 1 atm 298 Bruker AVANCE III 800 2 2D 1H-1H NOESY 1.06 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*G)-3'), 75 mM potassium chloride, 25 mM potassium phosphate 90% H2O/10% D2O 100 mM 7.0 1 atm 298 Bruker AVANCE III 800 3 2D 1H-1H NOESY 1.06 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*G)-3'), 75 mM potassium chloride, 25 mM potassium phosphate 90% H2O/10% D2O 100 mM 7.0 1 atm 283 Bruker AVANCE III 800
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 800
NMR Refinement Method Details Software simulated annealing X-PLOR NIH simulated annealing Amber molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 20 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment CcpNmr Analysis 2.4 CCPN 2 peak picking CcpNmr Analysis 2.4 CCPN 3 processing TopSpin Bruker Biospin 4 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman 5 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman 6 structure calculation X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore