| simulated annealing | TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING
NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS
3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL
J. MAGN. RESON. B104, 99-103 (1994).
TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB
CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999))
TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN
CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN
125, 171-177 (1997).
COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER
QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M,
GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988)
PROTEIN ENG. 2, 27-38).
THE 3D STRUCTURE OF THE OLIGOMERIZATION DOMAIN (RESIDUES
319 - 360) OF P53 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED
AND -FILTERED NMR IS BASED ON 4472 EXPERIMENTAL RESTRAINTS
COMPRISING THE FOLLOWING INTRA- AND INTER-SUBUNIT
RESTRAINTS:
(A) INTRASUBUNIT: 852 SEQUENTIAL (|I-J|=1), 712 MEDIUM
RANGE (1 < |I-J| >=5) AND 76 LONG RANGE (|I-J| >5)
INTERRESIDUES AND 740 INTRARESIDUE APPROXIMATE INTERPROTON
DISTANCE RESTRAINTS, 136 DISTANCE RESTRAINTS FOR 68
HYDROGEN BONDS, 284 TORSION ANGLE (144 PHI, 104 CHI1, AND
36 CHI2) RESTRAINTS, AND 144 THREE-BOND HN-HA COUPLING
CONSTANT RESTRAINTS.
(B) INTERSUBUNIT: 244 A-B/C-D, 876 A-C/B-D, 40 A-D/B-C
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 40 DISTANCE
RESTRAINTS FOR 20 HYDROGEN BONDS INVOLVING THE A-C/B-D
SUBUNITS, AND 36 DISTANCE RESTRAINTS FOR 4 WATER MOLECULES.
IN ADDITION, THERE ARE A TOTAL OF 38 CALPHA AND 35 CB
CHEMICAL SHIFT RESTRAINTS PER SUBUNIT THAT HAVE BEEN
INCORPORATED INTO THE REFINEMENT [J. KUSZWESKI, J. QIN,
A.M. GRONENBORN AND G.M. CLORE, J. MAGN RESON. SER B 106,
92-96 (1995)].
THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC
MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. &
GRONENBORN, A.M. (1988) FEBS LETT. 229, 317-324. ALL
STRUCTURAL STATISTICS ARE GIVEN IN THE SOURCE REFERENCE.
THIS ENTRY CONTAINS THE RESTRAINED MINIMIZED AVERAGE
STRUCTURE, FOLLOWED BY THE 22 INDIVIDUAL SIMULATED ANNEALING
STRUCTURES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAI
BY FIRST AVERAGING
COORDINATES OF THE INDIVIDUAL 22 DYNAMICAL SIMULATED
ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 326 - 354
OF ALL FOUR SUBUNITS, AND SUBJECTING THE RESULTING
COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY
PRESENTED IN COLUMNS 61 - 66 OF THE RESTRAINED MINIMIZED MEA
STRUCTURE
(THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE
AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES
AND THE MEAN STRUCTURE. THE NUMBERS IN COLUMNS 61 - 66 OF
THE INDIVIDUAL STRUCTURES HAVE NO MEANING. NOTE THAT
RESIDUES 319 - 323 AT THE N-TERMINUS AND RESIDUES 357 - 360
AT THE C-TERMINUS ARE COMPLETELY DISORDERED.
TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING:
NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS
3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL
J. MAGN. RESON. B104, 99-103 (1994).
TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB
CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999))
TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN
CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN
125, 171-177 (1997).
COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER
QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M,
GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988)
PROTEIN ENG. 2, 27-38).
THE 3D STRUCTURE OF THE OLIGOMERIZATION DOMAIN (RESIDUES
319 - 360) OF P53 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED
AND -FILTERED NMR IS BASED ON 4472 EXPERIMENTAL RESTRAINTS
COMPRISING THE FOLLOWING INTRA- AND INTER-SUBUNIT
RESTRAINTS:
(A) INTRASUBUNIT: 852 SEQUENTIAL (|I-J|=1), 712 MEDIUM
RANGE (1 < |I-J| >=5) AND 76 LONG RANGE (|I-J| >5)
INTERRESIDUES AND 740 INTRARESIDUE APPROXIMATE INTERPROTON
DISTANCE RESTRAINTS, 136 DISTANCE RESTRAINTS FOR 68
HYDROGEN BONDS, 284 TORSION ANGLE (144 PHI, 104 CHI1, AND
36 CHI2) RESTRAINTS, AND 144 THREE-BOND HN-HA COUPLING
CONSTANT RESTRAINTS.
(B) INTERSUBUNIT: 244 A-B/C-D, 876 A-C/B-D, 40 A-D/B-C
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 40 DISTANCE
RESTRAINTS FOR 20 HYDROGEN BONDS INVOLVING THE A-C/B-D
SUBUNITS, AND 36 DISTANCE RESTRAINTS FOR 4 WATER MOLECULES.
IN ADDITION, THERE ARE A TOTAL OF 38 CALPHA AND 35 CB
CHEMICAL SHIFT RESTRAINTS PER SUBUNIT THAT HAVE BEEN
INCORPORATED INTO THE REFINEMENT [J. KUSZWESKI, J. QIN,
A.M. GRONENBORN AND G.M. CLORE, J. MAGN RESON. SER B 106,
92-96 (1995)].
THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC
MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. &
GRONENBORN, A.M. (1988) FEBS LETT. 229, 317-324. ALL
STRUCTURAL STATISTICS ARE GIVEN IN THE SOURCE REFERENCE.
THIS ENTRY CONTAINS THE RESTRAINED MINIMIZED AVERAGE
STRUCTURE, FOLLOWED BY THE 22 INDIVIDUAL SIMULATED ANNEALING
STRUCTURES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAI
BY FIRST AVERAGING
COORDINATES OF THE INDIVIDUAL 22 DYNAMICAL SIMULATED
ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 326 - 354
OF ALL FOUR SUBUNITS, AND SUBJECTING THE RESULTING
COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY
PRESENTED IN COLUMNS 61 - 66 OF THE RESTRAINED MINIMIZED MEA
STRUCTURE
(THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE
AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES
AND THE MEAN STRUCTURE. THE NUMBERS IN COLUMNS 61 - 66 OF
THE INDIVIDUAL STRUCTURES HAVE NO MEANING. NOTE THAT
RESIDUES 319 - 323 AT THE N-TERMINUS AND RESIDUES 357 - 360
AT THE C-TERMINUS ARE COMPLETELY DISORDERED. | XPLOR/CNS |
