Complex of the first and second type III domains of human Fibronectin in solution
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | IPAP-HSQC | 1.0mM 1F3-2F3 U-15N, 150mM NaCl, 20mM NaPi pH 7.0, 95% H2O, 5% D2O | 95% H2O/5% D2O | 150mM NaCl, 20mM Na2HPO3 | 7.0 | ambient | 303 | |
| 2 | IPAP-HSQC | 0.6mM 1F3-2F3 U-15N, 150mM NaCl, 20mM NaPi pH 7.0, 4% Radially compressed polyacrylamide gel, 95% H2O, 5% D2O | 95% H2O/5% D2O | 150mM NaCl, 20mM Na2HPO3 | 7.0 | ambient | 303 | |
| 3 | Backbone chemical shift assignments | 0.6mM 1F3-2F3 U-15N, 150mM NaCl, 20mM NaPi pH 7.0, 4% Radially compressed polyacrylamide gel, 95% H2O, 5% D2O | 95% H2O/5% D2O | 150mM NaCl, 20mM Na2HPO3 | 7.0 | ambient | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Home-built | Home build | 750 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Rigid body docking with torsional flexibility at the interfacial amino acid sidechains | The structure was calculated by rigid body docking using ambiguous interdomain NOE-like restraints derived from chemical shift mapping of the interface and residual dipolar couplings of the complex. 7 residues from each domain were used for the ambiguous NOEs as well as 72 RDCs total. The refinement protocol was similar to that of Clore & Schwieters, JACS 125, 2902 | Omega |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | Structures forming a single cluster after imposing a 50% lowest energy cutoff |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 39 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | Omega | Beta 6.0.3b2 | GE/Bruker |
| 2 | processing | NMRPipe | 2.3 Rev2005.319.11.22 | Frank Delaglio, NIH/NIDDK,LCP |
| 3 | data analysis | PIPP | 4.3.7 | Dan Garrett, NIH/NIDDK/LCP |
| 4 | structure solution | XPLOR-NIH | 2.12 | Schwieters, Kuszewski, Tjandra, Clore NIH/NIDDK/LCP |
| 5 | refinement | XPLOR-NIH | 2.12 | Schwieters, Kuszewski, Tjandra, Clore NIH/NIDDK/LCP |
