2O9L

AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_C13-seperated[F1], C12-filtered[F2] NOESY	1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O	100% D2O	250 mM NaCl	6.9	ambient	318
2	3D_C13-seperated_NOESY	1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O	90% H2O/10% D2O	250 mM NaCl	6.9	ambient	303
3	3D_15N-seperated_NOESY	1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O	90% H2O/10% D2O	250 mM NaCl	6.9	ambient	303
4	2D_C12-filtered[F1,F2] NOESY	1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O	100% D2O	250 mM NaCl	6.9	ambient	318
5	2D_C12-filtered[F1] NOESY	1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O	100% D2O	250 mM NaCl	6.9	ambient	318

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DMX	600
2	Bruker	AVANCE	600
3	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing	The 20-structure ensemble refined with XPLOR-NIH (PDB ID: 2O8K) were then subjected to 20 ps of simulated annealing using the SANDER module of AMBER 7.0 with the 1994 force field (ff94) and the generalized Born solvent model. First, 0.5 ps of energy minimization was performed. Then simulated annealing was run from 300K to 0K using NMR distant and dihedral restraints, as well as a distance dependent dielectric and a nonbonding cutoff of 15A.	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	20
Conformers Submitted Total Number	19
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe	2.3	Delaglio et al. 1995
2	data analysis	NMRView	5.0.4	Johnson and Blevins. 1994
3	structure solution	CYANA	2.1	Guntert. 2004
4	refinement	X-PLOR	2.14	Schwieters et al. 2003
5	refinement	Amber	7.0	Case et al. 2002

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.