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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
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Experiment
1NRM
Gramicidin A in Dodecyl Phosphocholine Micelles (NMR)
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SOLUTION NMR Experimental Data
Experimental Details
Sample Conditions
Sample Contents
3.06MM GRAMICIDIN A
Solvent
n/a
Ionic Strength
n/a
pH
4.0
Pressure
AMBIENT
Temperature (K)
328
Experiment(s):
2D NOESY
Spectrometer Information
Manufacturer
Model
Field Strength
Varian
VXRS
500.0
NMR Refinement
Method
DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION
Details
THE STRUCTURE WAS MODELED USING 705 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.
NMR Ensemble Information
Conformers Submitted Total Number
1
Representative Model Choice Rationale
1
minimized average structure
Additional NMR Experimental Information
1
A 65MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED.
Computation: NMR Software
#
Classification
Software Name
Author
1
refinement
DISCOVER 97.2
BIOSYM/MSI
2
structure solution
VNMR 3.2
--
3
structure solution
FELIX 95.0
--
4
structure solution
DSPACE 4.0
--