SOLUTION NMR Experimental Data


Experimental Details
Sample Conditions
Sample Contents0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
Solventn/a
Ionic Strength40 mM
pH7.00
Pressure1
Temperature (K)308.00
Experiment(s):13C-HSQC-J-MODULATED, COSY, 13C-HSQC-F1- COUPLED, 15N-HSQC-F1- COUPLED, 2D NOESY
Spectrometer Information
Manufacturer Model Field Strength
Bruker DMX 600.0
Bruker DMX 750.0
NMR Refinement
Method SIMULATED ANNEALING IN TORSION ANGLE SPACE USING A SIXTH ORDER PREDICTOR-CORRECTOR METHOD WITH AUTOMATIC TIME STEP SELECTION (C. SCHWIETERS AND G.M. CLORE)
Details 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.
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
1 THE NUMBER OF CALCULATED CONFORMERS IS 20 WITH NOES AND DIPOLAR COUPLINGS AND 20 WITH DIPOLAR COUPLINGS ONLY
Computation: NMR Software
# Classification 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.
2 structure solution version: 1999.039.11.31 NMRPIPE 1.7 --
3 structure solution version: 2.4 XWINNMR --
4 structure solution version: 4.2.8 PIPP/CAPP --