2M8L
HIV capsid dimer structure
SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion | 1 |
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Scattering Type | x-ray |
Radiation/Neutron Source | APS |
Synchrotron | synchrotron |
Beamline Type | 12-ID-B |
Detector Type | PILATUS 2M |
Detector Manufacturer Details | |
Temperature (K) | 298 |
pH | 6.5 |
Numer of Time Frames Used | |
Protein Concentration Range (mg/mL) | 3.25 - 6.5 |
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 | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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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: 0.207 MODEL 2, weight: 0.204 MODEL 3, weight: 0.201 MODEL 4, weight: 0.197 MODEL 5, weight: 0.191 Ensemble 2: MODEL 6, weight: 0.225 MODEL 7, weight: 0.214 MODEL 8, weight: 0.203 MODEL 9, weight: 0.190 MODEL 10, weight: 0.168 Ensemble 3: MODEL 11, weight: 0.202 MODEL 12, weight: 0.201 MODEL 13, weight: 0.200 MODEL 14, weight: 0.199 MODEL 15, weight: 0.198 Ensemble 4: MODEL 16, weight: 0.283 MODEL 17, weight: 0.243 MODEL 18, weight: 0.203 MODEL 19, weight: 0.162 MODEL 20, weight: 0.109 Ensemble 5: MODEL 21, weight: 0.200 MODEL 22, weight: 0.200 MODEL 23, weight: 0.200 MODEL 24, weight: 0.200 MODEL 25, weight: 0.200 Ensemble 6: MODEL 26, weight: 0.209 MODEL 27, weight: 0.206 MODEL 28, weight: 0.201 MODEL 29, weight: 0.196 MODEL 30, weight: 0.187 Ensemble 7: MODEL 31, weight: 0.203 MODEL 32, weight: 0.202 MODEL 33, weight: 0.201 MODEL 34, weight: 0.199 MODEL 35, weight: 0.196 Ensemble 8: MODEL 36, weight: 0.190 MODEL 37, weight: 0.194 MODEL 38, weight: 0.198 MODEL 39, weight: 0.204 MODEL 40, weight: 0.214 Ensemble 9: MODEL 41, weight: 0.200 MODEL 42, weight: 0.200 MODEL 43, weight: 0.200 MODEL 44, weight: 0.200 MODEL 45, weight: 0.200 Ensemble 10: MODEL 46, weight: 0.200 MODEL 47, weight: 0.200 MODEL 48, weight: 0.200 MODEL 49, weight: 0.200 MODEL 50, weight: 0.200 Ensemble 11: MODEL 51, weight: 0.203 MODEL 52, weight: 0.202 MODEL 53, weight: 0.200 MODEL 54, weight: 0.199 MODEL 55, weight: 0.197 Ensemble 12: MODEL 56, weight: 0.200 MODEL 57, weight: 0.200 MODEL 58, weight: 0.200 MODEL 59, weight: 0.200 MODEL 60, weight: 0.200 Ensemble 13: MODEL 61, weight: 0.200 MODEL 62, weight: 0.200 MODEL 63, weight: 0.200 MODEL 64, weight: 0.200 MODEL 65, weight: 0.200 Ensemble 14: MODEL 66, weight: 0.179 MODEL 67, weight: 0.186 MODEL 68, weight: 0.196 MODEL 69, weight: 0.208 MODEL 70, weight: 0.232 Ensemble 15: MODEL 71, weight: 0.200 MODEL 72, weight: 0.200 MODEL 73, weight: 0.200 MODEL 74, weight: 0.200 MODEL 75, weight: 0.200 Ensemble 16: MODEL 76, weight: 0.200 MODEL 77, weight: 0.200 MODEL 78, weight: 0.200 MODEL 79, weight: 0.200 MODEL 80, weight: 0.200 Ensemble 17: MODEL 81, weight: 0.200 MODEL 82, weight: 0.200 MODEL 83, weight: 0.200 MODEL 84, weight: 0.200 MODEL 85, weight: 0.199 Ensemble 18: MODEL 86, weight: 0.200 MODEL 87, weight: 0.200 MODEL 88, weight: 0.200 MODEL 89, weight: 0.200 MODEL 90, weight: 0.200 Ensemble 19: MODEL 91, weight: 0.201 MODEL 92, weight: 0.201 MODEL 93, weight: 0.200 MODEL 94, weight: 0.200 MODEL 95, weight: 0.198 Ensemble 20: MODEL 96, weight: 0.200 MODEL 97, weight: 0.200 MODEL 98, weight: 0.200 MODEL 99, weight: 0.200 MODEL 100, weight: 0.200 | X-PLOR NIH |
NMR Ensemble Information | |
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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 | ||||
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# | 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. |