2B3W

NMR structure of the E.coli protein YbiA, Northeast Structural Genomics target ET24.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY	1mM YbiA, U-15N, 13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	100 mM NaCl	6.5	ambient	298
2	3D_13C-separated_NOESY	1mM YbiA, U-15N, 13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	100 mM NaCl	6.5	ambient	298
3	4D_13C-separated_NOESY	1mM YbiA, U-15N, 13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 100 % D2O	100% D2O	100 mM NaCl	6.5	ambient	298
4	HNHA	1mM YbiA, U-15N, 5%-13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	100 mM NaCl	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	750
3	Varian	INOVA	800

NMR Refinement
Method	Details	Software
distance geometry simulated annealing cns water refinement	THE STRUCTURES ARE BASED ON A TOTAL OF 1598 RESTRAINTS. 1298 are NOE-DERIVED; SEQUENTIAL [(I-J)=1] = 1; MEDIUM RANGE [1<(I-J)<5] = 498; LONG RANGE [(I-J)>=5] = 632; HYDROGEN BOND RESTRAINTS = 94 (2 PER H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 8.1 (RESIDES 2-164); DIHEDRAL-ANGLE RESTRAINTS = 206 (103 PHI, 103 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 10.0 (RESIDES 2-164); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 4.0; NUMBER OF STRUCTURES COMPUTED = 25; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 0; AVERAGE R.M.S. DISTANCE VIOLATION = 0.002 ANG. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 5.1; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 10; AVERAGE R.M.S. ANGLE VIOLATION = 0.06 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 15-162) = 0.87 ANG; ALL HEAVY ATOMS = 1.29 ANG; PROCHECK (RESIDUES 15-162): MOST FAVORED REGIONS = 87%; ADDITIONAL ALLOWED REGIONS = 10%; GENEROUSLY ALLOWED REGIONS = 2%; DISALLOWED REGIONS = 1%.	Sparky

NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	Sparky	3.1	T.D. Goddard, D.G. Kneller
2	processing	NMRPipe	Linux9	F. Delaglio, A. Bax
3	data analysis	AutoStructure	2.1.1	Y.J. Huang, G.T. Montelione
4	structure solution	X-PLOR	xplor-nih-2.10	C.D Schwieters, J.J.Kuszewski, N. Tjandra, G.M. Clore
5	refinement	CNS	1.1	A. Brunger, G.L. Warren
6	collection	VNMR	6.1c	Varian

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.