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THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS
SOLUTION NMR
NMR Refinement
Method
Details
Software
THE STRUCTURE IS BASED ON A TOTAL OF 223 NOE, 52 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 110 TORSION ANGLE RESTRAINTS, 101 CH DIPOLAR COUPLING RESTRAINTS. THE EXPERIMENTAL RESTRAINTS ARE ESSENTIALLY THE SAME AS THOSE LISTED IN N.SIBILLE,A.PARDI,J.P.SIMORRE,M.BLACKLEDGE J.AM.CHEM.SOC. V 123, 12135 2001. THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, A BASE-BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE.
X-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteria
RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers Calculated Total Number
250
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
THE DIPOLAR COUPLINGS WERE DIVIDED INTO 10 PAIRS
OF WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND
PARTITIONED IN A RATIO OF 70% (WORKING) AND
30% (TEST). 25 SIMULATED ANNEALING STRUCTURES
WERE CALCULATED FOR EACH PAIR, RESULTING IN A TOTAL
OF 250 STRUCTURES. THE STRUCTURE REPORTED HERE IS
OBTAINED BY RESTRAINED REGULARIZED OF THE MEAN
COORDINATES OF THE ENSEMBLE OF 250 INDIVIDUAL
SIMULATED ANNEALING STRUCTURES CALCULATED WITH
COMPLETE DIPOLAR COUPLING CROSS-VALIDATION.
FOR THE ENSEMBLE OF 250 STRUCTURES THE WORKING
DIPOLAR COUPLING R-FACTOR IS 8.6+/-0.5% AND
THE FREE DIPOLAR COUPLING R-FACTOR IS 26.8+/-2.8%.