7V06 | pdb_00007v06

Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for differential binding of hnRNP Splicing Auxiliary Factors

SOLUTION NMR - SOLUTION SCATTERING

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Solution Scattering Data Acquistion	1
Scattering Type	neutron
Radiation/Neutron Source	APS BioCat 18ID beam line
Synchrotron	Y
Beamline Type	APS
Detector Type
Detector Manufacturer Details
Temperature (K)	298
pH	6.2
Numer of Time Frames Used
Protein Concentration Range (mg/mL)	6-6.5
Sample Buffer	20 mM Bis-Tris, 20 mM NaCl, pH 6.2
Data Reduction Software	GNOM
Guiner Mean Radius Of Gyration (nm)	2.1
Sigma Mean Radius Of Gyration	0.1
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)	6.9

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
NMR, SAXS	NMRpipe, NMRViewJ ,X-PLOR_NIH, AMBER, GNOM	Frank Delaglio; Ad Bax; Bruce Johnson; Charles Schwieters; Marius Clore; David Case; Dmitry Svergun		1024	10	Lowest energy	10

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	400 uM ESS2p	90% H2O/10% D2O	5 mM	6.5	1 atm	283	Bruker AVANCE NEO 700
2	2D 1H-13C HMQC	400 uM [U-100% 13C; U-100% 15N on ATP and GTP ESS2p	100% D2O	5 mM	6.5	1 atm	298	Bruker AVANCE II 900
3	2D 1H-1H NOESY	450 uM selective deuteration ESS2p	100% D2O	5 mM	6.5	1 atm	298	Bruker AVANCE II 800
4	2D 1H-1H TOCSY	400 uM ESS2p	90% H2O/10% D2O	5 mM	6.5	1 atm	298	Bruker AVANCE II 800
5	2D 1H-15N HSQC	300 uM Uniform_15N on GTP and UTP ESS2p	90% H2O/10% D2O	5 mM	6.5	1 atm	283	Bruker AVANCE II 800
6	2D 1H-15N HNN-COSY	300 uM Uniform_15N on all nucleotides ESS2p	90% H2O/10% D2O	5 mM	6.5	1 atm	283	Bruker AVANCE II 900

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE II	900
2	Bruker	AVANCE II	800
3	Bruker	AVANCE NEO	700

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	1024
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
2	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
3	chemical shift assignment	NMRViewJ		Bruce Johnson
4	collection	TopSpin		Bruker Biospin
5	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	data analysis	NMRFAM-SPARKY		Woonghee Lee, Marco Tonelli, John L Markley