Solution structure of 7SK stem-loop 1 with HEXIM Arginine Rich Motif
SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion | 1 |
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Scattering Type | neutron |
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Radiation/Neutron Source | 12.3.1 (SIBYLS) beam line |
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Synchrotron | Y |
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Beamline Type | 12.3.1 |
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Detector Type | Pilatus3 X 2M detector |
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Detector Manufacturer Details | Dectris |
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Temperature (K) | 283 |
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pH | 5.6 |
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Numer of Time Frames Used | 10 |
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Protein Concentration Range (mg/mL) | |
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Sample Buffer | 10 mM phosphate, 70 mM NaCl, 0.1 mM EDTA |
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Data Reduction Software | ATSAS |
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Guiner Mean Radius Of Gyration (nm) | 2.2 |
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Sigma Mean Radius Of Gyration | |
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R(XS-1) Mean Cross Sectional Radii (nm) | |
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R(XS-1) Sigma Mean Cross Sectional Radii | |
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R(XS-2) Mean Cross Sectional Radii (nm) | |
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R(XS-2) Sigma Mean Cross Sectional Radii | |
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P(R) Protein Length (nm) | |
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Solution Scattering Data Analysis and Model Fitting |
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Method | Software | Software Authors | Starting Model | Conformers, Number Calculated | Conformers, Number Submitted | Conformers, Selection Criteria | Best Representative Conformer | Other Details |
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This structure was calculated with XPLOR-NIH with a CYANA input and minimized with SAXS. | | | | | | | | |
NMR Experiment |
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
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1 | 2D 1H-1H NOESY | 0.5 mM HEXIM, 0.5 mM 7SK | 100% D2O | 70mM NaCl, 0.1mM EDTA mM | 5.6 | 100000 Pa | 298 | Bruker DMX 700 |
2 | 2D 1H-1H NOESY | 0.5 mM HEXIM, 0.5 mM 7SK | 90% H2O/10% D2O | 70mM NaCl, 0.1mM EDTA mM | 5.6 | 100000 Pa | 298 | Bruker DMX 700 |
3 | 2D 1H-13C HSQC | 0.5 mM [U-100% 13C; U-100% 15N] HEXIM, 0.5 mM 7SK | 90% H2O/10% D2O | 70mM NaCl, 0.1mM EDTA mM | 5.6 | 100000 Pa | 298 | Bruker DMX 700 |
4 | 2D 1H-13C HSQC | 0.5 mM HEXIM, 0.5 mM [U-100% 13C; U-100% 15N] 7SK | 90% H2O/10% D2O | 70mM NaCl, 0.1mM EDTA mM | 5.6 | 100000 Pa | 298 | Bruker DMX 700 |
5 | 2D 1H-13C HSQC aliphatic | 0.5 mM HEXIM, 0.5 mM [U-100% 13C; U-100% 15N] 7SK | 100% D2O | 70mM NaCl, 0.1mM EDTA mM | 5.6 | 100000 Pa | 298 | Bruker DMX 700 |
6 | 2D 1H-13C HSQC aliphatic | 0.5 mM [U-100% 13C; U-100% 15N] HEXIM, 0.5 mM 7SK | 100% D2O | 70mM NaCl, 0.1mM EDTA mM | 5.6 | 100000 Pa | 298 | Bruker DMX 700 |
NMR Spectrometer Information |
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Spectrometer | Manufacturer | Model | Field Strength |
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1 | Bruker | DMX | 700 |
NMR Refinement |
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Method | Details | Software |
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simulated annealing | | X-PLOR NIH |
NMR Ensemble Information |
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Conformer Selection Criteria | structures with the lowest energy |
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Conformers Calculated Total Number | 100 |
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Conformers Submitted Total Number | 10 |
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Representative Model | 1 (lowest energy) |
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Computation: NMR Software |
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# | Classification | Version | Software Name | Author |
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1 | collection | TopSpin | | Bruker Biospin |
2 | peak picking | NMRView | | Johnson, One Moon Scientific |
3 | chemical shift assignment | NMRView | | Johnson, One Moon Scientific |
4 | data analysis | CYANA | | Guntert, Mumenthaler and Wuthrich |
5 | processing | CYANA | | Guntert, Mumenthaler and Wuthrich |
6 | structure calculation | CYANA | | Guntert, Mumenthaler and Wuthrich |
7 | structure calculation | X-PLOR NIH | | Schwieters, Kuszewski, Tjandra and Clore |
8 | refinement | X-PLOR NIH | | Schwieters, Kuszewski, Tjandra and Clore |