2B3W
NMR structure of the E.coli protein YbiA, Northeast Structural Genomics target ET24.
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 750 |
3 | Varian | INOVA | 800 |
NMR Refinement | ||
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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 | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | 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 |