| REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE
STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE
GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD
(M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229,
317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER,
YALE UNIVERSITY, CT 06511).
STRUCTURAL STATISTICS
RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)*
RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS)
ALL 513 0.079
INTERRESIDUE
SHORT RANGE 150 0.086
INTERRESIDUE
LONG RANGE 105 0.100
INTRARESIDUE 234 0.065
HBOND *(2)* 24 0.043
POTENTIAL ENERGY TERMS
TYPE ENERGY (KCAL/MOL)
F(NOE) *(3)* 160
F(TOR) *(4)* 24
F(REPEL) *(5)* 72
LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED
USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS
-117 KCAL/MOL.
DEVIATIONS FROM IDEALIZED GEOMETRY *(6)*
TYPE TOTAL NUMBER RMS DEVIATION
BONDS 646 0.013 (ANGSTROMS)
ANGLES 1157 2.517 (DEGREES)
IMPROPERS 242 0.797 (DEGREES)
NOTES.
*(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS
ARE CALCULATED WITH RESPECT TO THE UPPER AND
LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF
THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN
0.5 ANGSTROMS.
*(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO
RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND
R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS
ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII
OF THE RELEVANT ATOMS.
*(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL
F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF
50 KCAL/MOL/ANGSTROM**2.
*(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE
CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A
SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO
RESTRICT THE RANGES OF 23 PHI AND 21 CHI1 TORSION
ANGLES, AND THE OMEGA PEPTIDE BOND TORSION ANGLES
OF THE FIVE PROLINE RESIDUES (PRO 36 AND 42 BEING
RESTRAINED TO THE CIS CONFORMATION AND THE OTHERS
TO TRANS).
*(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM
F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF
4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE
VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD
VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY
FUNCTION.
*(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY
AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE
PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION
OF PROLINES) IN THE TRANS CONFORMATION. IN THE
DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE
RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED
IN THE BOND AND ANGLE TERMS.
A TOTAL OF 42 STRUCTURES CONSISTENT WITH THE NMR DATA
WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES
OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL
STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO
FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THESE
42 STRUCTURES ARE GIVEN IN THE PDB ENTRY *2BDS*.
THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE
ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT
THE MEAN COORDINATE POSITIONS.
ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS
ARE AVAILABLE IN THE PDB NMR RESTRAINT FILE. | XPLOR |
