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Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4 93% H2O/7% D2O 20 6.8 ambient 298.2 2 2D 1H-15N HSQC 1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8 93% H2O/7% D2O 20 6.8 ambient 298.2
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing TopSpin
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 10 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Additional NMR Experimental Information Details Two titration experiments were conducted. Basically unlabeled ligand protein was added stepwise to N15-Labeled protein solution.
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin 2.1 Bruker Biospin 2 processing TopSpin 2.1 Bruker Biospin 3 chemical shift assignment CARA 1.8.1 Keller and Wuthrich 4 geometry optimization HADDOCK 2.1 Alexandre Bonvin 5 refinement HADDOCK 2.1 Alexandre Bonvin 6 structure solution HADDOCK 2.1 Alexandre Bonvin