7AFQ
Ribosome binding factor A (RbfA)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
2 | 3D HNCO | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
3 | 3D HNCA | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
4 | 3D HNCACB | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
5 | 3D CBCA(CO)NH | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
6 | 3D HN(CO)CA | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
11 | 3D HNCAHA | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
10 | 3D HCCH-TOCSY | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 600 |
9 | 3D HN(CA)CO | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
8 | 3D HNH NOESY | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
7 | 3D CNH NOESY | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
13 | 3D HN(CO)CAHA | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | Bruker AVANCE III 800 |
12 | 3D HCH NOESY | 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP | 90% H2O/10% D2O | 40 mM | 7.6 | 1 atm | 293 | 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 |
simulated annealing | X-PLOR NIH | |
molecular dynamics | GROMACS |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 60 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | chemical shift assignment | Sparky | Goddard | |
3 | chemical shift assignment | CcpNmr Analysis | CCPN | |
4 | peak picking | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
6 | refinement | GROMACS | Emile Apol, Rossen Apostolov, Paul Bauer, Herman J.C. Berendsen, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Rudi van Drunen, Anton Feenstra, Alan Gray, Gerrit Groenhof, Anca Hamuraru, Vincent Hindriksen M. Eric Irrgang, Aleksei Iupinov, Christoph Junghans, Joe Jordan, Dimitrios Karkoulis, Peter Kasson,, Jiri Kraus, Carsten Kutzner, Per Larsson, Justin A. Lemkul, Viveca Lindahl, Magnus Lundborg, Erik Marklund, Pascal Merz, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alexey Shvetsov, Alfons Sijbers, Peter Tieleman, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov. |