1OSR
Structural study of dna duplex containaing a n-(2-deoxy-beta-erytho-pentofuranosyl) formamide frameshift by nmr and restrained molecular dynamics
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | NOESY | 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA | 99.9% D2O | 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA | 6.5 | AMBIENT | 290 | |
2 | COSY | 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA | 99.9% D2O | 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA | 6.5 | AMBIENT | 290 | |
3 | DQFCOSY | 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA | 99.9% D2O | 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA | 6.5 | AMBIENT | 290 | |
4 | TOCSY | 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA | 99.9% D2O | 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA | 6.5 | AMBIENT | 290 | |
5 | HSQC 1H-31P | 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA | 99.9% D2O | 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA | 6.5 | AMBIENT | 290 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
MOLECULAR MODELING; SIMULATED ANNEALING; RESTRAINED MOLECULAR DYNAMICS SIMULATIONS | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 2 |
Representative Model | 2 (those which were used to initiate molecular dynamic simulations) |
Additional NMR Experimental Information | |
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Details | THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. TWO REPRESENTATIVE STRUCTURES OF THE TWO ISOMER CIS AND TRANS FOR THE FORMAMIDE RESIDUE ARE PRESENTED. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | KOLLMAN | |
2 | refinement | MORCAD | LEBRET | |
3 | refinement | MOLMOL | 2.6 | Koradi, Wuthrich |
4 | processing | XwinNMR | 2.5 | BRUKER |