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THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID CRYSTALLINE PHASE
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
13C-HSQC-J-MODULATED
0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
40 mM
7.00
1 atm
308.00
2
COSY
0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
40 mM
7.00
1 atm
308.00
3
13C-HSQC-F1- COUPLED
0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
40 mM
7.00
1 atm
308.00
4
15N-HSQC-F1- COUPLED
0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
40 mM
7.00
1 atm
308.00
5
2D NOESY
0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
40 mM
7.00
1 atm
308.00
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX
600
2
Bruker
DMX
750
NMR Refinement
Method
Details
Software
SIMULATED ANNEALING IN TORSION ANGLE SPACE
USING A SIXTH ORDER PREDICTOR-CORRECTOR METHOD
WITH AUTOMATIC TIME STEP SELECTION
(C. SCHWIETERS AND G.M. CLORE)
THE STRUCTURE IS BASED ON A
TOTAL OF 162 NOE, 48 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 137 DIHEDRAL
137 TORSION ANGLE RESTRAINTS, 198 CH AND 10 NH ONE-BOND DIPOLAR
COUPLING RESTRAINTS, AND 200 APPROXIMATE PROTON-PROTON
DIPOLAR COUPLINGS. THE EXPERIMENTAL RESTRAINTS ARE THE SAME AS THOSE
LISTED IN 1DUF. THE NON-BONDED CONTACTS ARE REPRESENTED
BY A QUARTIC VAN DER WAALS REPULSION TERM AND A BASE-BASE POSITIONING
DATABASE POTENTIAL OF MEAN FORCE. ALSO INCLUDED IS A TORSION ANGLE
DATABASE POTENTIAL OF MEAN FORCE.
IN THIS ENTRY THE SECOND TO LAST COLUMN REPRESENTS THE
AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED
ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS.
MODEL 1 IS CALCULATED WITH NOE-DERIVED INTERPROTON
DISTANCE RESTRAINTS, DIPOLAR COUPLING
RESTRAINTS AND TORSION ANGLE RESTRAINTS.
MODEL 2 IS CALCULATED WITH DIPOLAR COUPLING AND TORSION
ANGLE RESTRAINTS. NO NOE-DERIVED INTERPROTON
DISTANCE RESTRAINTS WERE EMPLOYED.
STRUCTURAL STATISTICS:
----------------------------------------------------------
RESTRAINTS MODEL 1 MODEL 2
(# MODEL 1/# MODEL 2) (NOE + DIPOLARS) (DIPOLARS ONLY)
----------------------------------------------------------
RMS DEVIATIONS FROM EXPERIMENTAL RESTRAINTS
INTERPROTON DISTANCES (A) 0.065 0.114
(162/0)
TORSION ANGLES (DEG) 0 0
(137/137)
ALL DIPOLAR COUPLINGS (HZ) 2.8 2.6
(408/408)
RMS DEVIATIONS AND DIPOLAR COUPLING R-FACTORS
FOR DIFFERENT CLASSES OF DIPOLAR COUPLINGS
C-H RIBOSE (HZ/%) (94/94)* 2.27 (11.4%) 2.27 (11.4%)
C-H RIBOSE (HZ/%) (64/64)** 5.62 (28.1%) 5.24 (26.2%)
C-H BASE (HZ/%) (24/24)* 2.78 (13.9%) 2.81 (14.1%)
C-H BASE (HZ/%) (12/12)** 1.89 (9.26%) 2.01 (10.0%)
C-H METHYL (HZ/%) (4/4)* 0.98 (4.9%) 0.79 (4.0%)
N-H IMINO (HZ/%) (10/10)* 1.56 (15.9%) 1.50 (15.2%)
H-H ABSOLUTE VALUE (HZ)
(126/126) 1.26 1.25
H-H SIGN KNOWN (HZ) (74/74) 0.93 0.88
RMS DEVIATIONS FROM IDEALIZED COVALENT GEOMETRY
BONDS (A) 0.003 0.003
ANGLES (DEG) 0.897 0.925
IMPROPER TORSIONS (DEG) 0.296 0.106
----------------------------------------------------------
* MEASURED WITH AN ACCURACY OF +/- 2 HZ
** MEASURED WITH AN ACCURACY OF +/- 4 HZ
DIPOLAR COUPLING R-FACTOR = RATIO RMS DEVIATION BETWEEN
OBSERVED AND CALCULATED VALUES AND EXPECTED RMS DEVIATION
IF VECTORS ARE RANDOMLY DISTRIBUTED. THE LATTER IS GIVEN
BY {2DA**2[4 + 3H**2]/5}1/2 WHERE DA IS THE MAGNITUDE OF
THE AXIAL COMPONENT OF THE ALIGNMENT TENSOR AND H IS THE
RHOMBICITY. (ONLY APPLIES TO FIXED LENGTH VECTORS). THE
VALUES OF DA(CH), DA(NH) AND H ARE -16 HZ, -7.7 HZ AND
0.26, RESPECTIVELY.
NIH VERSION OF XPLOR (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN pub/clore/xplor_nih)
NMR Ensemble Information
Conformer Selection Criteria
THE RESTRAINED REGULARIZED MEAN STRUCTURES
Conformers Calculated Total Number
40
Conformers Submitted Total Number
2
Additional NMR Experimental Information
Details
THE NUMBER OF CALCULATED CONFORMERS IS 20 WITH NOES AND DIPOLAR COUPLINGS
AND 20 WITH DIPOLAR COUPLINGS ONLY
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
refinement
NIH VERSION OF XPLOR (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN pub/clore/xplor_nih)
CLORE, SCHWIETERS AND KUSZEWSKI. ADAPTED FROM XPLOR 3.841 by BRUNGER ET AL.