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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