| 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 578 0.024
INTERRESIDUE
SHORT RANGE 206 0.030
INTERRESIDUE
LONG RANGE 137 0.017
INTRARESIDUE 211 0.021
HBOND *(2)* 24 0.019
POTENTIAL ENERGY TERMS
TYPE ENERGY (KCAL/MOL)
F(NOE) *(3)* 17
F(TOR) *(4)* 0
F(REPEL) *(5)* 34
LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED
USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS
-118 KCAL/MOL.
DEVIATIONS FROM IDEALIZED GEOMETRY *(6)*
TYPE TOTAL NUMBER RMS DEVIATION
BONDS 503 0.010 (ANGSTROMS)
ANGLES 896 2.170 (DEGREES)
IMPROPERS 227 0.911 (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 33 PHI ,24 PSI AND 25 CHI1
TORSION ANGLES.
*(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 41 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 THE
41 STRUCTURES ARE GIVEN IN THE PROTEIN DATA BANK ENTRY
*2CBH*.
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 RESTRAINT FILE. | XPLOR |
