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NMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomyces cerevisiae
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 2 2D 1H-13C HSQC aliphatic 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 3 2D 1H-13C HSQC aromatic 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 4 3D HCCH-TOCSY 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 16 3D CBCA(CO)NH 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 800 17 3D HNCACB 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 800 18 3D HNCO 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 5 3D HBHA(CO)NH 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 10 3D C(CO)NH 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 9 3D H(CCO)NH 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 8 3D 1H-13C NOESY aliphatic 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Bruker AVANCE III 900 7 3D 1H-13C NOESY aromatic 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Bruker AVANCE III 900 13 2D 1H-15N HSQC 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 11 2D 1H-15N HSQC 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 279 Varian VXRS 600 12 2D 1H-15N HSQC 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 283 Varian VXRS 600 14 2D 1H-15N HSQC 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 283 Bruker AVANCE III 600 15 2D 1H-15N HSQC 93% H2O/7% D2O 150 NaCl mM 7.5 1 atm 283 Bruker AVANCE III 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 900 2 Varian VXRS 800 3 Varian VXRS 600 4 Bruker AVANCE III 600
NMR Refinement Method Details Software simulated annealing Final step with explicit water refinement PONDEROSA-C/S
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)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 collection VNMR Varian 3 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 peak picking NMRFAM-SPARKY 1.41 Lee, Tonelli and Markley 5 peak picking APES Shin, Lee and Lee 6 chemical shift assignment NMRFAM-SPARKY 1.41 Lee, Tonelli and Markley 7 chemical shift assignment PINE Bahrami, Markley, Assadi, and Eghbalnia 8 chemical shift assignment PINE-SPARKY Lee, Westler, Bahrami, Eghbalnia and Markley 9 structure calculation PONDEROSA-C/S Lee, Stark and Markley 10 structure calculation AUDANA Lee, Petit, Cornilescu, Stark and Markley 11 structure calculation X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 12 refinement PONDEROSA-C/S Lee, Stark and Markley 13 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore