2KRL

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.