2JS7

Solution NMR structure of human myeloid differentiation primary response (MyD88). Northeast Structural Genomics target HR2869A

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	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
2	2D 1H-13C HSQC	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
3	3D HNCACB	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
4	3D HNCO	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
5	3D HNCA	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
6	3D HN(COCA)CB	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
7	3D HN(CO)CA	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
8	3D HN(CA)CO	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
9	3D HBHA(CO)NH	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
10	3D 1H-13C NOESY	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
11	3D 1H-15N NOESY	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
12	3D HCCH-COSY	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
13	3D HCCH-TOCSY	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
14	3D CCH-TOCSY	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
15	2D 1H-13C HSQC stereospecific VL	0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
16	3D 1H-13C NOESY	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	100% D2O		5.0	ambient	303
17	2D 1H-13C HSQC	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	100% D2O		5.0	ambient	303
18	H/D exch	0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	100% D2O		5.0	ambient	303
19	HETnoe	0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303
20	T1/T2	0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile	95% H2O/5% D2O		5.0	ambient	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing	MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR T1/T2. MEASURED TC = 12.1 +/- 1NS AT 20DEG. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA AND AUTOSTRUCTURE IN A CONSENSUS APPROACH. SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED WITH CYANA, LOWEST ENERGY SELECTED IN AUTOSTRUCTURE USING NIH-XPLOR FOR SIMULATEED ANNEALING MD. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.36%, SIDECHAIN 95.8%, AROMATIC (SC) 93.1%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2795 NOE. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.35 A (1MODEL). 16 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELIX (28-39, 68-71, 81-85, 87-99, 103-106, 141-150), BETA-STRAND (48-49, 17-22, 72-78, 108-112, 130-131) [S(PHI)+ (PSI)] > 1.8. RMSD 0.6 BB, 0.9 ALL HEAVY ATOMS. RAMACHANDRAN: 88.0% MOST FAV, 11.4% ADDTL ALLOW, 0.5 GENEROUS ALLOW, 0.1% DISALLOW. PROCHECK (PSI-PHI): -0.22/-0.55 (RAW/Z), PROCHECK (ALL): -0.15/-0.89 (RAW/Z), MOLPROBITY CLASH: 27.22/-3.15 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.934, PRECISION: 0.892, F-MEASURE: 0.913, DP-SCORE: 0.721.	CYANA

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	structure solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
2	structure solution	AutoStructure	2.1.1	Huang, Tejero, Powers and Montelione
3	chemical shift assignment	AutoAssign	1.14	Zimmerman, Moseley, Kulikowski and Montelione
4	data analysis	Sparky	2.110	Goddard
5	processing	NMRPipe	2005	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	collection	TopSpin	1.3	Bruker Biospin
7	visualization	MOLMOL	2K.2	Koradi, Billeter and Wuthrich
8	validation	PSVS	1.3	Bhattacharya and Montelione
9	validation	ProcheckNMR		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th
10	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
11	refinement	X-PLOR NIH	2.11.2	Schwieters, Kuszewski, Tjandra and Clore
12	validation	MolProbity		Richardson