1MFJ
3' Stem-Loop from Human U4 SNRNA
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride | D2O | 10 mM sodium phosphate & 50 mM NaCl | 6.4 | ambient | 303 | |
2 | 2D NOESY | 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride | 90% H2O/10% D2O | 10 mM sodium phosphate & 50 mM NaCl | 6.4 | ambient | 293 | |
3 | DQF-COSY | 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride | D2O | 10 mM sodium phosphate & 50 mM NaCl | 6.4 | ambient | 303 | |
4 | 2D TOCSY | 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride | D2O | 10 mM sodium phosphate & 50 mM NaCl | 6.4 | ambient | 303 | |
5 | natural abundance 13C-HMQC | 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride | D2O | 10 mM sodium phosphate & 50 mM NaCl | 6.4 | ambient | 303 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
complete relaxation matrix; random error analysis of NOE; torsion angle dynamics; simulated annealing using Metropolis Monte Carlo; restrained minimization | Structures 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 | |
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Conformer Selection Criteria | Lowest total energy (a weighted sum of conformational energy and restraint energy). |
Conformers Calculated Total Number | 15 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest total energy) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques and complete relaxation matrix analysis of NOE intensities. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 6.1 | Varian Associates, Inc. |
2 | processing | NMRPipe | 2.1 | Delaglio |
3 | data analysis | Sparky | 3.0 | Goddard & Kneller |
4 | iterative matrix relaxation | MARDIGRAS | 3.2 | Borgias et al. |
5 | refinement | DYANA | 1.5 | Guentert |
6 | refinement | miniCarlo | Ulyanov et al. |