1YCW
Clustered abasic lesions in dna: nmr solution structures of clustered bistranded-1 abasic lesion
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2mM DUPLEX, 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA | 25 mM PHOSPHATE BUFFER; PH 6.8; 50 mM NaCl; 0.5 mM EDTA. | NOT DETERMINED | 6.8 | AMBIENT | 298 | |
2 | 2D TOCSY | 2mM DUPLEX, 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA | 25 mM PHOSPHATE BUFFER; PH 6.8; 50 mM NaCl; 0.5 mM EDTA. | NOT DETERMINED | 6.8 | AMBIENT | 298 | |
3 | DQF-COSY | 2mM DUPLEX, 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA | 25 mM PHOSPHATE BUFFER; PH 6.8; 50 mM NaCl; 0.5 mM EDTA. | NOT DETERMINED | 6.8 | AMBIENT | 298 | |
4 | COSY, COSY45 | 2mM DUPLEX, 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA | 25 mM PHOSPHATE BUFFER; PH 6.8; 50 mM NaCl; 0.5 mM EDTA. | NOT DETERMINED | 6.8 | AMBIENT | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 500 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
RESTRAINED MOLECULAR DYNAMICS | 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO 300K IN 40PS. 4) EQUILIBRATION STAGE: 120PS DYNAMICS AT 300K | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 5 |
Representative Model | 1 (closest to the average) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.1 | A. BRUNGER |
2 | data analysis | Felix | 98 | |
3 | data analysis | INSIGHT 95, MIDAS PLUS, CURVES 5 |