2KQM
Solution structure of the KI O18/O8 Y87H immunoglobulin light chain variable domain
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 | 0.8 mM [U-100% 13C; U-100% 15N] kI O18/O8 Y87H-1, 10 mM [U-2H] MES-2, 0.02 % sodium azide-3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 8 | 6.8 | AMBIENT | 298 | |
2 | 3D_13C-separated_NOESY | 0.8 mM [U-100% 13C; U-100% 15N] kI O18/O8 Y87H-1, 10 mM [U-2H] MES-2, 0.02 % sodium azide-3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 8 | 6.8 | AMBIENT | 298 | |
3 | 3D_13C-separated_NOESY (AROMATIC) | 0.8 mM [U-100% 13C; U-100% 15N] kI O18/O8 Y87H-1, 10 mM [U-2H] MES-2, 0.02 % sodium azide-3, 95% H2O, 5% D2O | 95% H2O/5% D2O | 8 | 6.8 | AMBIENT | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | Avance II | 600 |
NMR Refinement | ||
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Method | Details | Software |
AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 2477 NOE CONSTRAINTS (410 INTRA, 489 SEQUENTIAL, 340 MEDIUM, 1214 INTRAMONOMER LONG RANGE AND 24 INTERMONOMER NOE CONSTRAINTS) AND 151 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS PER MONOMER. CONSTRAINTS WERE ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINTS IN THE SECOND MONOMER. | Xplor-NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Xplor-NIH | 2.9.3 | SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. |
2 | collection | TopSpin | 2.1 | Bruker |
3 | processing | nmrPipe | 2007 | Delagio,F. et al. |
4 | data analysis | XEASY | 1.3 | Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. |
5 | data analysis | GARANT | 2.1 | C. Bartels |
6 | structural calculation | Cyana | 2.1 | Guntert, P. |