1D8B
NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_13C-SEPARATED_NOESY | 13C-15N-LABELED SAMPLE | 20 mM sodium phosphate buffer | 20 mM SODIUM PHOSPHATE | 6.5 | 1 bar | 295 | |
| 2 | 3D_15N-SEPARATED_NOESY | 15N-LABELED SAMPLE | 20 mM sodium phosphate buffer | 20 mM SODIUM PHOSPHATE | 6.5 | 1 bar | 295 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| ARIA (AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENTS) AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS | STARTING WITH AN ALMOST COMPLETE LIST OF CHEMICAL SHIFTS, THE PROGRAM ARIA ( AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENT) CALIBRATES NOES, MERGES THE OBTAINED AMBIGUOUS DISTANCE RESTRAINTS FROM DIFFERENT NOE SPECTRA AND ASSIGNS THE NOE PEAKS IN AN ITERATIVE MANNER. FROM A TOTAL OF 1890 NOES ABOUT 85% WERE MANUALLY ASSIGNED, THE REMAINDER WAS ASSIGNED BY ARIA. FLOATING POINT CHIRALITY ASSIGNMENT WAS USED DURING THE STRUCTURE CALCULATION IN ORDER TO OBTAIN STEREOSPECIFIC ASSIGNMENTS FOR METHYL AND METHYLENE GROUPS. THEREFORE, SOME METHYL AND METHYLENE CARBON/PROTON ATOM NAMES IN THE RESTRAINT FILES MIGHT BE INCONSISTENT COMPARED TO THOSE IN THE COORIDINATE FILES. THE DEPOSITED STRUCTURES HAVE BEEN WATER-REFINED AS DESCRIBED IN THE PUBLICATION. PSI REFINEMENT: THE STRUCTURES HAVE BEEN DIRECTLY REFINED AGAINST CROSS- CORRELATED RELAXATION RATES (C-ALPHA-H-ALPHA DIPOLE, CO CSA) AND THE THREE- BOND H/D ISOTOPE EFFECT ON THE C-ALPHA CHEMICAL SHIFT. "REFINEMENT OF THE PROTEIN BACKBONE ANGLE PSI IN NMR STRUCTURE CALCULATIONS." SPRANGERS, BOTTOMLEY, LINGE, SCHULTZ, NILGES, SATTLER. | NMRPipe |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | 1.7 | DELAGLIO |
| 2 | data analysis | XEASY | 1.3.13 | BARTELS, XIA, BILLETER, GUENTERT, WUETHRICH |
| 3 | structure solution | ARIA | 0.9 | LINGE, O'DONOGHUE, NILGES |
| 4 | iterative matrix relaxation | ARIA | 0.9 | LINGE, O'DONOGHUE, NILGES |
| 5 | structure solution | CNS | 0.9 | BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARREN |
| 6 | refinement | CNS | 0.9 | BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARREN |
