1KDL | pdb_00001kdl

Solution structure of the amphipathic domain of YopD from Yersinia

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE	50% H2O; 10 D2O; 40% TFE	20 mM SODIUM PHOSPHATE BUFFER	4.5	1 atm	313
2	2D TOCSY	3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE	50% H2O; 10 D2O; 40% TFE	20 mM SODIUM PHOSPHATE BUFFER	4.5	1 atm	313
3	DQF-COSY	3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE	50% H2O; 10 D2O; 40% TFE	20 mM SODIUM PHOSPHATE BUFFER	4.5	1 atm	313
4	15N HSQC	3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE	50% H2O; 10 D2O; 40% TFE	20 mM SODIUM PHOSPHATE BUFFER	4.5	1 atm	313
5	13C HSQC	3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE	50% H2O; 10 D2O; 40% TFE	20 mM SODIUM PHOSPHATE BUFFER	4.5	1 atm	313

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600
2	Bruker	AMX	500

NMR Refinement
Method	Details	Software
simulated annealing	STANDARD SIMULATED ANNEALING PROTOCOL USING XPLOR 3.851. DIHEDRAL RESTRAINTS WERE OBTAINED WITH TALOS	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number	150
Conformers Submitted Total Number	1
Representative Model	1 (n/a)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.851	Brunger
2	data analysis	XwinNMR	2.6	Bruker
3	iterative matrix relaxation	MARDIGRAS	3.0	Borgias
4	data analysis	TALOS	98.040.21.02	Cornilescu