6CCX

NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N TROSY	0.2 mM U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC	90% H2O/10% D2O	105 mM	7.4	1 atm	298	Bruker AVANCE II 800
2	2D 1H-15N TROSY	0.2 mM GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC, 0.4 mM PE-DTPA-Gd	90% H2O/10% D2O	105 mM	7.4	1 atm	298	Bruker AVANCE II 800
4	2D 1H-13C HMQC	0.2 mM U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC	90% H2O/10% D2O	105 mM	7.4	1 atm	298	Bruker AVANCE II 800
3	2D 1H-13C HMQC	0.2 mM GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC, 0.4 mM PE-DTPA-Gd	90% H2O/10% D2O	105 mM	7.4	1 atm	298	Bruker AVANCE II 800

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

NMR Refinement
Method	Details	Software
simulated annealing		TopSpin

NMR Ensemble Information
Conformer Selection Criteria	10 structures for lowest energy
Conformers Calculated Total Number	3000
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	HADDOCK modelling consists of (I) rigid-body docking, (II) a semi-flexible refinement stage, and (III) final refinement in explicit solvent (final gentle water). The starting structure is 2MSE. Distance restraints are based on PRE, NOE and CSP.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	Sparky		Goddard
5	structure calculation	HADDOCK		Bonvin
6	refinement	HADDOCK		Bonvin
7	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
8	chemical shift assignment	Sparky		Goddard