1O15
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%. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR NIH | (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) | CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA |
