2M8P
The structure of the W184AM185A mutant of the HIV-1 capsid protein
SOLUTION NMR - SOLUTION SCATTERING
| Solution Scattering Data Acquistion | 1 |
|---|---|
| Scattering Type | x-ray |
| Radiation/Neutron Source | APS |
| Synchrotron | synchrotron |
| Beamline Type | 12-ID-B |
| Detector Type | mosaic Gold CCD |
| Detector Manufacturer Details | |
| Temperature (K) | 298 |
| pH | 6.5 |
| Numer of Time Frames Used | |
| Protein Concentration Range (mg/mL) | 0.63 - 5.0 |
| Sample Buffer | |
| Data Reduction Software | |
| Guiner Mean Radius Of Gyration (nm) | |
| Sigma Mean Radius Of Gyration | |
| 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) |
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 2 | 2D 1H-13C HSQC | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 3 | 2D 1H-13C HSQC aliphatic | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 4 | 2D 1H-13C HSQC aromatic | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 5 | 3D HNCO | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 6 | 3D HNCACB | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 7 | 3D HNCA | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 8 | 3D HN(CO)CA | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 9 | 3D 1H-15N NOESY | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 10 | 2D TROSY-Artsy | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 11 | 2D 1H-15N R1 | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 12 | 2D 1H-15N R1 | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 13 | 2D 1H-15N R1r | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 14 | 2D 1H-15N R1r | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 15 | 2D 1H-15N HetNOE | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| 16 | 2D 1H-15N HetNOE | 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate | 95% H2O/5% D2O | 6.5 | ambient | 308 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | This is an ensemble refinement. The MODEL entries appear in groups of 5, representing 20 ensembles. Xplor-NIH Ensemble Calculation This file contains 20 ensembles of size 5 Ensemble 1: MODEL 1, weight: 0.379 MODEL 2, weight: 0.272 MODEL 3, weight: 0.185 MODEL 4, weight: 0.114 MODEL 5, weight: 0.050 Ensemble 2: MODEL 6, weight: 0.355 MODEL 7, weight: 0.267 MODEL 8, weight: 0.191 MODEL 9, weight: 0.126 MODEL 10, weight: 0.062 Ensemble 3: MODEL 11, weight: 0.347 MODEL 12, weight: 0.265 MODEL 13, weight: 0.193 MODEL 14, weight: 0.130 MODEL 15, weight: 0.066 Ensemble 4: MODEL 16, weight: 0.207 MODEL 17, weight: 0.205 MODEL 18, weight: 0.201 MODEL 19, weight: 0.197 MODEL 20, weight: 0.190 Ensemble 5: MODEL 21, weight: 0.221 MODEL 22, weight: 0.212 MODEL 23, weight: 0.203 MODEL 24, weight: 0.191 MODEL 25, weight: 0.173 Ensemble 6: MODEL 26, weight: 0.364 MODEL 27, weight: 0.269 MODEL 28, weight: 0.189 MODEL 29, weight: 0.121 MODEL 30, weight: 0.057 Ensemble 7: MODEL 31, weight: 0.220 MODEL 32, weight: 0.212 MODEL 33, weight: 0.203 MODEL 34, weight: 0.191 MODEL 35, weight: 0.173 Ensemble 8: MODEL 36, weight: 0.366 MODEL 37, weight: 0.269 MODEL 38, weight: 0.188 MODEL 39, weight: 0.120 MODEL 40, weight: 0.056 Ensemble 9: MODEL 41, weight: 0.219 MODEL 42, weight: 0.212 MODEL 43, weight: 0.203 MODEL 44, weight: 0.192 MODEL 45, weight: 0.174 Ensemble 10: MODEL 46, weight: 0.264 MODEL 47, weight: 0.234 MODEL 48, weight: 0.204 MODEL 49, weight: 0.172 MODEL 50, weight: 0.127 Ensemble 11: MODEL 51, weight: 0.233 MODEL 52, weight: 0.219 MODEL 53, weight: 0.204 MODEL 54, weight: 0.186 MODEL 55, weight: 0.159 Ensemble 12: MODEL 56, weight: 0.218 MODEL 57, weight: 0.211 MODEL 58, weight: 0.203 MODEL 59, weight: 0.192 MODEL 60, weight: 0.175 Ensemble 13: MODEL 61, weight: 0.096 MODEL 62, weight: 0.122 MODEL 63, weight: 0.159 MODEL 64, weight: 0.221 MODEL 65, weight: 0.403 Ensemble 14: MODEL 66, weight: 0.333 MODEL 67, weight: 0.260 MODEL 68, weight: 0.196 MODEL 69, weight: 0.137 MODEL 70, weight: 0.074 Ensemble 15: MODEL 71, weight: 0.083 MODEL 72, weight: 0.109 MODEL 73, weight: 0.149 MODEL 74, weight: 0.218 MODEL 75, weight: 0.442 Ensemble 16: MODEL 76, weight: 0.256 MODEL 77, weight: 0.231 MODEL 78, weight: 0.204 MODEL 79, weight: 0.175 MODEL 80, weight: 0.134 Ensemble 17: MODEL 81, weight: 0.298 MODEL 82, weight: 0.248 MODEL 83, weight: 0.201 MODEL 84, weight: 0.154 MODEL 85, weight: 0.098 Ensemble 18: MODEL 86, weight: 0.223 MODEL 87, weight: 0.214 MODEL 88, weight: 0.203 MODEL 89, weight: 0.190 MODEL 90, weight: 0.170 Ensemble 19: MODEL 91, weight: 0.097 MODEL 92, weight: 0.122 MODEL 93, weight: 0.159 MODEL 94, weight: 0.221 MODEL 95, weight: 0.401 Ensemble 20: MODEL 96, weight: 0.334 MODEL 97, weight: 0.261 MODEL 98, weight: 0.196 MODEL 99, weight: 0.136 MODEL 100, weight: 0.073 | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 480 |
| Conformers Submitted Total Number | 100 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR NIH | 2.32 | Schwieters, Kuszewski, Tjandra and Clore |
| 2 | collection | TopSpin | 1.3 | Bruker Biospin |
| 3 | data analysis | CCPN-Analysis | 2.2.2 | (CCPN-Analysis)-Vranken, Boucher, Stevens..Laue. |
