2L08
Solution NMR Structure of Nonsense mRNA reducing factor 3A from H. Sapiens, Northeast Structural Genomics Consortium Target HR4714B
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 | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
2 | 2D 1H-15N HSQC | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
3 | 2D 1H-13C HSQC | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
4 | 2D 1H-13C HSQC | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
5 | 2D 1H-13C HSQC | 0.9 mM [U-10% 13C; U-99% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
6 | 3D CBCA(CO)NH | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
7 | 3D HNCO | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
8 | 3D HNCA | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
9 | 3D HNCACB | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
10 | 3D HBHA(CO)NH | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
11 | 3D C(CO)NH-TOCSY | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
12 | 3D CCH-TOCSY | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
13 | 3D HNHA | 0.9 mM [U-10% 13C; U-99% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
14 | 3D simul NOESY | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 | |
15 | 3D arom NOESY | 0.82 mM [U-100% 13C; U-100% 15N] HR4714B | 90% H2O/10% D2O | 100mM NaCl, 10mM Tris-HCl | 7.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Final structure quality (excluding 10 residue tag) determined using PSVS-v1.4: Ordered residues are defines as: 10-19,22-34,36-45,54-72,76-94. (a) RMSD (ordered residues) all backbone aroms: 0.6A. and heavy atoms 1.0A. (b) Ramachandran statistics for ordered residues: Most favored region: 85.1% Additionally favored region: 14.8% Generaously allowed region: 0.1% Disallowed region: 0.1%. (c) Procheck scores for ordered residues (RAW/Z): Phi/psi -0.73/-2.56, all -0.65/-3.84, (d) Molprobity clashscores (RAW/Z)22.41/-2.32 (e) RPF scores for the goodness fit to NOESY data: Recall: 89, Precision: 94, F-measure: 92, final dp-score - (f) RMS deviation for bond angles - 6.15, RMS deviation for bond lengths 0.01A. | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The Structure was obtained using triple resonance NMR spectroscopy for backbone and side chain assignments. Automated NOESY assignments were made using Autostructure and CYANA3.0. Dihedral angle constraints were obtained using TALOS. The structure calculation was done excluding the 10-residue N-terminal tag. Completeness of assignment excluding the tag: Backbone - 80%, Sidechain - 80%. Peaks for 13 residues in NHSQC spectra are missing due to line broadening. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | 2.0.6 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
3 | structure solution | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
4 | chemical shift assignment | PINE | Bahrami, Markley, Assadi, and Eghbalnia |