| simulated annealing | THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING
THE PROGRAM X-PLOR MODIFIED TO INCORPORATE DIPOLAR
COUPLING RESTRAINTS (TJANDRA ET AL. (1997) NATURE STRUCT
BIOL 4, 732-738) AND A CONFORMATIONAL DATABASE POTENTIAL
FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. (1996)
PROTEIN SCI 5, 1067 - 1080 AND (1997) J. MAGN. RESON. 125,
171-177). THE EXPERIMENTAL RESTRAINTS ARE GIVEN IN
R2GATMR.
THE STRUCTURES ARE BASED ON A TOTAL OF 1830 EXPERIMENTAL
NMR RESTRAINTS COMPRISING: 1444 INTERPROTON DISTANCE
RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 296 TORSION
ANGLE RESTRAINTS; 90 RESIDUAL DIPOLAR COUPLINGS (52 N-H
AND 38 C-H). THE NOE RESTRAINTS ARE SUBDIVIDED AS FOLLOWS:
(A) WITHIN THE PROTEIN: 242 INTERRESIDUE SEQUENTIAL
(|I-J|=1); 161 INTERRESIDUE SHORT RANGE (1(LESS
THAN)|I-J|(LESS THAN)=5); 182 INTERRESIDUE LONG RANGE
(|I-J|(GREATER THAN)5); AND. 334 INTRARESIDUE. (B) WITHIN
THE DNA: 157 INTRARESIDUE; 180 SEQUENTIAL INTRASTRAND; 34
INTERSTRAND; AND 37. H-BONDS (C) BETWEEN PROTEIN AND DNA:
117. THE TORSION ANGLE RESTRAINTS ARE SUBDIVIDED AS
FOLLOWS: 144 ANGLES FOR THE PROTEIN (58 PHI, 56 PSI, 26
CHI1 AND 4 CHI2) AND. 152 FOR THE DNA. THE TORSION ANGLE
RESTRAINTS FOR THE DNA COMPRISE LOOSE RESTRAINTS ON THE
BACKBONE TORSION ANGLES ALPHA, BETA, GAMMA, EPSILON AND
ZETA TO PREVENT PROBLEMS ASSOCIATED WITH LOCAL MIRROR
IMAGES.
THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED
MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE
RMS OF THE 34 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
FOUND IN PDB ENTRY 3GAT ABOUT THE MEAN COORDINATE
POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA
STRUCTURES HAS NO MEANING.
THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL
AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR:
POINT 1 50.250 -27.763 2.413
POINT 2 50.328 -26.611 3.418 | X-PLOR |
