1JO3

Gramicidin B in Sodium Dodecyl Sulfate Micelles (NMR)


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY5MM GRAMICIDIN B, 250MM DEUTERATED SODIUM DODECYL SULFATE, 80% 100MM PHOSPHATE BUFFER PH 6.5, 10% D2O, 10% DEUTERATED TFE6.5AMBIENT328
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianVXRS500
NMR Refinement
MethodDetailsSoftware
DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATIONTHE STRUCTURE WAS MODELED USING 622 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 TO EMULATE THAT OF THE MICELLE INTERIOR.DISCOVER 97.2
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number1
Representative Model (minimized average structure)
Additional NMR Experimental Information
DetailsA 40MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementDISCOVER 97.2BIOSYM/MSI
2structure solutionVNMR 3.2
3structure solutionFELIX 95.0
4structure solutionDSPACE 4.0