SOLUTION NMR

NMR Experiment
Experiment Type Sample Contents Ionic Strength Solvent pH Pressure Temprature (K)
1 2D 1H-1H TOCSY 0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3'), 90% H2O/10% D2O 130 90% H2O/10% D2O 6.85 ambient 298
2 2D 1H-1H COSY 0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3'), 90% H2O/10% D2O 130 90% H2O/10% D2O 6.85 ambient 298
3 2D 1H-1H NOESY 0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3'), 90% H2O/10% D2O 130 90% H2O/10% D2O 6.85 ambient 298
NMR Spectrometer Information
Spectrometer Manufacturer Model Field Strength
1 Bruker AVANCE 500
NMR Refinement
Method Details Software
simulated annealing DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE CLASSIFIED ACCORDING TO CROSSPEAK INTENSITIES AS (S) STRONG (1.80 TO 2.90), (M) MEDIUM (1.80 TO 4.00) AND (W) WEAK (D = 4.0, -2.2/+1.0 ). DISTANCE CONSTRAINS WITH METHYL PROTONS WERE CONSIDERED SEPARATELY (D = 4.0 , -2.2/+1.5 ). THE SIMULATED ANNEALING APPROACH WAS USED TO GENERATE 200 STRUCTURES. THE 10 LOWEST ENERGY STRUCTURES WERE CHOSEN AND THE ROOT MEAN SQUARE DEVIATION VALUES CALCULATED. 1
NMR Ensemble Information
Conformer Selection Criteria structures with the lowest energy
Conformers Calculated Total Number 200
Conformers Submitted Total Number 10
Representative Model 1 (lowest energy)
Computation: NMR Software
# Classification Version Software Name Author
1 refinement 2.16 X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore
2 collection 1.3 TopSpin Bruker Biospin
3 processing 1.3 TopSpin Bruker Biospin
4 peak picking 3.5.5 AMIX Bruker Biospin
5 chemical shift assignment 3.5.5 AMIX Bruker Biospin