1MFJ

3' Stem-Loop from Human U4 SNRNA


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chlorideD2O10 mM sodium phosphate & 50 mM NaCl6.4ambient303
22D NOESY1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride90% H2O/10% D2O10 mM sodium phosphate & 50 mM NaCl6.4ambient293
3DQF-COSY1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chlorideD2O10 mM sodium phosphate & 50 mM NaCl6.4ambient303
42D TOCSY1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chlorideD2O10 mM sodium phosphate & 50 mM NaCl6.4ambient303
5natural abundance 13C-HMQC1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chlorideD2O10 mM sodium phosphate & 50 mM NaCl6.4ambient303
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA600
NMR Refinement
MethodDetailsSoftware
complete relaxation matrix; random error analysis of NOE; torsion angle dynamics; simulated annealing using Metropolis Monte Carlo; restrained minimizationStructures are based on 200 distance restraints, of which 140 are quantitative bounds for nonexchangeable protons calculated with MARDIGRAS, 56 are upper bounds for exchangeable protons, and 4 are hydrogen bond restraints.VNMR
NMR Ensemble Information
Conformer Selection CriteriaLowest total energy (a weighted sum of conformational energy and restraint energy).
Conformers Calculated Total Number15
Conformers Submitted Total Number10
Representative Model1 (lowest total energy)
Additional NMR Experimental Information
DetailsThis structure was determined using standard 2D homonuclear techniques and complete relaxation matrix analysis of NOE intensities.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionVNMR6.1Varian Associates, Inc.
2processingNMRPipe2.1Delaglio
3data analysisSparky3.0Goddard & Kneller
4iterative matrix relaxationMARDIGRAS3.2Borgias et al.
5refinementDYANA1.5Guentert
6refinementminiCarloUlyanov et al.