Solution NMR Structure of CAPER RRM2 Domain. Northeast Structural Genomics Target HR4730A
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D 1H-15N NOESY | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 2 | 3D 1H-13C NOESY | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 3 | 2D 1H-13C HSQC | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 4 | 2D 1H-15N HSQC | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 5 | 2D 1H-13C HSQC stereospecific methyl | 1.1 mM [U-5% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 6 | HETnoe | 1.1 mM [U-5% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 7 | 3D HNCACB | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 8 | 3D HN(COCA)CB | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 9 | 3D HNCO | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 10 | 3D HBHA(CO)NH | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 11 | 3D HCCH-TOCSY | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 12 | 3D HCCH-COSY | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| 13 | 3D CCH-TOCSY | 1.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT | 95% H2O/5% D2O | 0.1 | 6.5 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | AutoAssign | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CHEMICAL SHIFTS (TALOS) FOR DIHEDRAL ANGLE INFERENCE, AND DYANA FOR SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED. CONVERGED STRUCTURES ARE FURTHER REFINED USING NIH-XPLOR FOLLOWED BY CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING N-TERM TAG): BACKBONE 99.19%, SIDECHAIN 94.31%, AROMATIC (SC) 100%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1252 NOE, 44 H-BOND, 84 DIHEDRAL. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.30 A (1 MODEL), MAX DIHEDRAL VIOLATION 4.0 DEG. 5 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED RESIDUES RANGES - ALPHA HELIX (40-47, 78-88), B-STRAND (53-61, 66-75, 27-32, 99-101) [S(PHI)+S(PSI)] > 1.8. RMSD 0.4 BB, 1.0 ALL HEAVY ATOMS. RAMACHANDRAN: 85.4% MOST FAV, 12.4% ADDTL ALLOW, 2.3 GENEROUSLY ALLOW, 0.0% DISALLOW. PROCHECK (PSI-PHI): -0.46/-1.49 (RAW/Z), PROCHECK (ALL): -0.24/-1.42 (RAW/Z), MOLPROBITY CLASH: 15.06/-1.06 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.959, PRECISION: 0.935, F-MEASURE: 0.947, DP-SCORE: 0.775. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | AutoAssign | 2.3.0 | Zimmerman, Moseley, Kulikowski and Montelione |
| 2 | structure solution | AutoStructure | 2.1.1 | Huang, Tejero, Powers and Montelione |
| 3 | processing | NMRPipe | 2.4 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 4 | data analysis | Sparky | 2.112 | Goddard |
| 5 | collection | TopSpin | 1.3 | Bruker Biospin |
| 6 | refinement | CNSSOLVE | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 7 | refinement | X-PLOR NIH | 2.11.2 | Schwieters, Kuszewski, Tjandra and Clore |
| 8 | structure solution | DYANA | Guntert, Mumenthaler and Wuthrich | |
| 9 | validation | PSVS | 1.3 | Bhattacharya and Montelione |
| 10 | data analysis | PdbStat | 5.0 | (PDBStat) Tejero |
| 11 | visualization | MOLMOL | 2K.2 | Koradi, Billeter and Wuthrich |
| 12 | validation | MolProbity | Richardson | |
| 13 | validation | ProcheckNMR | Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th | |
