Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data
SOLUTION NMR - SOLUTION SCATTERING
| Solution Scattering Data Acquistion | 1 |
|---|---|
| Scattering Type | x-ray |
| Radiation/Neutron Source | Bruker NanostarU TXS |
| Synchrotron | N |
| Beamline Type | |
| Detector Type | AXS Vantec 2000 |
| Detector Manufacturer Details | Bruker |
| Temperature (K) | 288 |
| pH | 4.5 |
| Numer of Time Frames Used | 10 |
| Protein Concentration Range (mg/mL) | 7 - 10 |
| Sample Buffer | ACETATE |
| Data Reduction Software | SAXS for Windows XP |
| Guiner Mean Radius Of Gyration (nm) | 31 |
| Sigma Mean Radius Of Gyration | 0.01 |
| R(XS-1) Mean Cross Sectional Radii (nm) | |
| R(XS-1) Sigma Mean Cross Sectional Radii | |
| R(XS-2) Mean Cross Sectional Radii (nm) | |
| R(XS-2) Sigma Mean Cross Sectional Radii | |
| P(R) Protein Length (nm) | 121 |
| Solution Scattering Data Analysis and Model Fitting | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Method | Software | Software Authors | Starting Model | Conformers, Number Calculated | Conformers, Number Submitted | Conformers, Selection Criteria | Best Representative Conformer | Other Details | |||||||||||
| CONSTRAINED SCATTERING FITTING INCORPORATING NMR RDC DATA. | VMD, GNOM, OLIGOMER | UIUC, EMBL | 5953 | 1 | THE MODELS WERE GENERATED USING GRID SEARCH, CONTRAINING THE ORIENTATION BETWEEN THE DIMERS ACCORDING TO NMR RDC DATA. MODELS WERE THEN SCORED BASED ON AGREEMENT BETWEEN THEORETICAL AND EXPERIMENTAL SCATTERING CURVE AND SOUNDNESS OF THE INTERFACE AS DEFINED BY A RESIDUE PAIRING SCORE. | 1 | PDB CODE 1U4L | ||||||||||||
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N J-mod TROSY | 1 mM [U-100% 15N] ccl5, 50 mM sodium acetate | 90% H2O/10% D2O | 0.05 | 4.4 | ambient | 297 | |
| 2 | 2D 1H-15N TROSY | 1 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide | 90% H2O/10% D2O | 0.05 | 4.4 | ambient | 297 | |
| 3 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide | 90% H2O/10% D2O | 0.05 | 4.4 | ambient | 297 | |
| 4 | 2D 1H-15N J-mod TROSY | 1 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide | 90% H2O/10% D2O | 0.05 | 4.4 | ambient | 297 | |
| 5 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] ccl5, 50 mM sodium acetate | 90% H2O/10% D2O | 0.05 | 4.4 | ambient | 297 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 800 |
| 2 | Varian | INOVA | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics, SAXS-potential guided scoring within grid search | NAMD | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function based on SAXS & knowledge-based potential |
| Conformers Calculated Total Number | 1 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (best agreement with data) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | NAMD | Phillips, Braun, Wang, Gumbart, Tajkhorshid, Villa, Chipot, Skeel, Kale, and Schulte | |
| 2 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 3 | collection | VnmrJ | Varian | |
| 4 | refinement | VMD | Humphrey, Dalke & Schulten. | |
