SOLUTION NMR Experimental Data


NMR Refinement
Method MOLECULAR DYNAMICS, MATRIX RELAXATION
Details THREE STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITOMYCIN C ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES DERIVED FROM NMR DATA. THE THREE DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL THREE STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 90, 120, 200 AND 300 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE THREE FINAL STRUCTURES ARE: MDL1 MDL2 MDL3 R(1/6) FACTOR 0.027 0.026 0.026 BOND (ANG) 0.008 0.008 0.008 ANGLE (DEG) 2.913 2.931 2.949 IMPROPER (DEG) 0.361 0.393 0.372
NMR Ensemble Information
Conformer Selection Criteria all calculated structures submitted
Conformers Calculated Total Number 3
Conformers Submitted Total Number 3
Computation: NMR Software
# Classification Software Name Author
1 refinement X-PLOR BRUNGER