2LP1 | pdb_00002lp1

The solution NMR structure of the transmembrane C-terminal domain of the amyloid precursor protein (C99)

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC-TROSY	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318
2	3D HNCA	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318
3	3D HNCACB	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318
4	3D HN(CO)CA	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318
5	3D HN(COCA)CB	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318
6	3D HNCO	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318
7	3D gnoesyNhsqc	10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA	90% H2O/10% D2O		6.5	ambient	318

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AMX	800
2	Bruker	AMX	600
3	Varian	INOVA	900

NMR Refinement
Method	Details	Software
molecular dynamics, simulated annealing	RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING, FOLLOWED BY POWELL ENERGY MINIMIZATION	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	30
Representative Model	1 (closest to the average)

Additional NMR Experimental Information
Details	All 2D and 3D experiments were TROSY based. For the RDC data collection, the TROSY/Semi-TROSY method was used.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR NIH	2.24	Schwieters, Kuszewski, Tjandra and Clore
2	refinement	X-PLOR NIH	2.24	Schwieters, Kuszewski, Tjandra and Clore
3	data analysis	NMRDraw	Linux9	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	Sparky	3.114	Goddard
5	chemical shift assignment	Sparky	3.114	Goddard
6	peak picking	Sparky	3.114	Goddard
7	processing	NMRPipe	Linux9	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
8	geometry optimization	TALOS	Linux9	Cornilescu, Delaglio and Bax
9	structure solution	TALOS	Linux9	Cornilescu, Delaglio and Bax
10	data analysis	ProcheckNMR	3.5.4	Laskowski and MacArthur
11	structure solution	ProcheckNMR	3.5.4	Laskowski and MacArthur
12	collection	TopSpin	3	Bruker Biospin