6QH2
Solution NMR ensemble for a chimeric KH-S1 domain construct of exosomal polynucleotide phosphrylase at 298K compiled using the CoMAND method
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D HNCACB | 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride | 90% H2O/10% D2O | 125 mM | 7.5 | ambient atm | 298 | Bruker AVANCE III 600 |
2 | 3D CBCA(CO)NH | 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride | 90% H2O/10% D2O | 125 mM | 7.5 | ambient atm | 298 | Bruker AVANCE III 600 |
3 | 3D C(CO)NH | 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride | 90% H2O/10% D2O | 125 mM | 7.5 | ambient atm | 298 | Bruker AVANCE III 600 |
4 | 3D HCCH-TOCSY | 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride | 90% H2O/10% D2O | 125 mM | 7.5 | ambient atm | 298 | Bruker AVANCE III 600 |
5 | 3D CNH-NOESY | 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride | 90% H2O/10% D2O | 125 mM | 7.5 | ambient atm | 298 | Bruker AVANCE III 800 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 600 |
2 | Bruker | AVANCE III | 800 |
NMR Refinement | ||
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Method | Details | Software |
R-factor based frame picking | frames picked from unrestrained MD simulations to minimise overall CNH-NOESY based R-Factors | CoMAND |
NMR Ensemble Information | |
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Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
Conformers Calculated Total Number | 10000 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | structure calculation | Shine | Riss & Coles | |
2 | structure calculation | Rosetta | 3.6 | Das & Baker |
5 | refinement | NAMD | 2.12 | University of Illinois |
6 | refinement | CoMAND | in house |