1LPW
Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1mM U2 snRNA-intron duplex; 10mM sodium phosphate | 90% H2O/10% D2O | 50mM sodium chloride | 6.4 | ambient | 278 | |
2 | 2D NOESY | 1mM U2 snRNA-intron duplex; 10mM sodium phosphate | 100% D2O | 50mM sodium chloride | 6.4 | ambient | 293 | |
3 | 2D TOCSY | 1mM U2 snRNA-intron duplex; 10mM sodium phosphate | 100% D2O | 50mM sodium chloride | 6.4 | ambient | 293 | |
4 | DQF-COSY | 1mM U2 snRNA-intron duplex; 10mM sodium phosphate | 100% D2O | 50mM sodium chloride | 6.4 | ambient | 293 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | UNITYPLUS | 720 |
2 | Varian | UNITYPLUS | 720 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
torsion angle molecular dynamics followed by conjugate gradient minimization | A total of 191 distance restraints were used, not including the 40 hydrogen bond distances imposed. Including the 133 dihedral restraints applied in structure calculations, 353 total restraints were applied. | VNMR |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | lowest energy structures that did not violate data from fluorescence experiments |
Conformers Calculated Total Number | 800 |
Conformers Submitted Total Number | 9 |
Representative Model | 2 (lowest energy structure that agreed best with experimental data) |
Additional NMR Experimental Information | |
---|---|
Details | This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times, so that the buildup of certain NOEs could be observed to resolve some spectral overlap. |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 5.3 | Varian, Inc. |
2 | data analysis | Sparky | 3.69 | T.D. Goddard and D.G. Kneller |
3 | structure solution | VNMR | 3.851 | Axel Brunger |
4 | refinement | X-PLOR | 3.851 | Brunger |