The ensemble of the solution global structures of the 102-nt ribosome binding structure element of the turnip crinkle virus 3' UTR RNA
SOLUTION NMR - SOLUTION SCATTERING
| Solution Scattering Data Acquistion | 1 |
|---|---|
| Scattering Type | x-ray |
| Radiation/Neutron Source | APS ARGONNE |
| Synchrotron | Y |
| Beamline Type | 12-ID,18-ID |
| Detector Type | MARCCD 165 |
| Detector Manufacturer Details | MARRESEARCH GMBH, GERMANY |
| Temperature (K) | 298 |
| pH | 6.8 |
| Numer of Time Frames Used | 20 |
| Protein Concentration Range (mg/mL) | 1.0-5.0 |
| Sample Buffer | 50 MM TRIS, 0.5 MM MgCl2 |
| Data Reduction Software | MARDETECTOR, HOME-WRITTEN PROGRAM |
| Guiner Mean Radius Of Gyration (nm) | 30.9 |
| Sigma Mean Radius Of Gyration | 0.4 |
| R(XS-1) Mean Cross Sectional Radii (nm) | |
| R(XS-1) Sigma Mean Cross Sectional Radii | |
| R(XS-2) Mean Cross Sectional Radii (nm) | |
| R(XS-2) Sigma Mean Cross Sectional Radii | |
| P(R) Protein Length (nm) | 110 |
| Solution Scattering Data Analysis and Model Fitting | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Method | Software | Software Authors | Starting Model | Conformers, Number Calculated | Conformers, Number Submitted | Conformers, Selection Criteria | Best Representative Conformer | Other Details | |||||||||||
| SIMULATED ANNEALING METHOD WITH RESTRAINTS OF X-RAY SCATTERING DATA, RDC DATA, GENERIC A-FORM GEOMETRIC DISTANCE IN DUPLEXES, GENERIC A-FORM LIKE STACKING, NMR DETECTED HYDROGEN BONDS, AND SAXS MOLECULAR ENVELOPE DIMENISIONAL MEASUREMENTS. | G2G, DAMMIN AND DAMAVER IN ATSAS 2.1, XPLOR-NIH | G2G INITIAL STRUCTURE | 100 | 10 | STRUCTURES WITH LOWEST TOTAL ENERGY. THE TOTAL ENERGY INCLUDES PSEUDO-POTENTIALS OF SCATTERING TERM, RDC TERM, HYDROGEN BONDING TERM, AND OTHER REGULAR PSEUDO-POTENTIALS IMPLEMENTED IN XPLOR-NIH. | 1 | SAXS MOLECULAR ENVELOPE WAS GENERATED USING AB INITIO MODEL CONSTRUCTION FROM SAXS BY DAMMIN AND DAMAVER. G2G WAS USED TO GENERATE INITIAL STRUCTURE. ... | SAXS MOLECULAR ENVELOPE WAS GENERATED USING AB INITIO MODEL
CONSTRUCTION FROM SAXS BY DAMMIN AND DAMAVER. G2G WAS USED TO GENERATE INITIAL STRUCTURE.
REFERENCE OF G2G IS : X. Zuo, J. Wang, P. Yu, D. Eyler, H. Xu, M.R. Starich, D.M. Tiede, A.E. Simon,
W. Kasprzak, C.D. Schwieters, B.A. Shapiro, Y.-X. WANG, A Method for Helical RNA
Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and
NMR Measurements; JOURNAL OF MOLECULAR BIOLOGY 2009, 393(3), 717-734. | |||||||||||
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.3-0.8 mM RNA-3 | 90% H2O/10% D2O | 50 | 6.8 | ambient | 298.2 | |
| 2 | 2D HNN-COSY | 0.3-0.8 mM [U-98% 15N] RNA-2 | 90% H2O/10% D2O | 50 | 6.8 | ambient | 298.2 | |
| 3 | IPAP-HSQC | 0.5 mM [U-98% 15N] RNA-4 | 90% H2O/10% D2O | |||||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, duplex-orientation restrained | the orientations of all duplexes were restrained during the SA calculation | G2G |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (closest to the average) |
| Additional NMR Experimental Information | |
|---|---|
| Details | MORE DETAILS ON STRUTURE DETERMINATION IN REMARK 265 |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | generate global structure of rnas | G2G | 1.0 | (G2G) J. Wang, X. Zuo and Y-X. Wang |
| 2 | refinement | X-PLOR NIH | 2.22 | Schwieters, Kuszewski, Tjandra and Clore |
