Experiment: 2KA3

Structure of EMILIN-1 C1Q-like domain

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D 15N-NOESY-HSQC	0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3	95% H2O/5% D2O	0.15	7.5	ambient	310
2	IPAP 1H,15N-HSQC	0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%)	95% H2O/5% D2O	0.15	7.5	ambient	310
3	TROSY 1H-15N HSQC	0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%)	95% H2O/5% D2O	0.15	7.5	ambient	310
4	3D HNCO	0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%)	95% H2O/5% D2O	0.15	7.5	ambient	310

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	GE	OMEGA	500
2	GE	OMEGA	600
3	GE	OMEGA	750
4	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
simulated annealing, restrained energy minimization	The structure was obtained as the refinement of the homology model of emilin trimer C1q-domain based on the chain A of ACRP-30 crystal structure. The quaternary structure of C1q-domain homology model was built with a three-fold simmetry axis. The region between Tyr927 and Gly945 was not modelled and was not included in the refinement. Dihedral angles (obtained with TALOS), RDC values, NOE constraints were used in the refinement procedure. The structures were further refined in order to improve the quality of backbone geometry. For this purpose 2,000 steps of restrained energy minimization were performed using the program NAMD (Kale et al. 1999). The forcefield used is CHARMM v.27b (MacKerell et al. 1998) with the CMAP correction (MacKerell et al., 2004). Since the program does not readily incorporate RDC derived restraints, the z co-ordinates of the backbone amide N and H atoms were restrained at their starting values. Only NOE derived restraints and chemical-shift-derived dihedral angle restraints (with unequivocal secondary structure definition) were imposed.	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.0	Bruker Biospin
2	data analysis	Felix	2.3	Accelrys Software Inc.
3	data analysis	XEASY	1.2	Bartels et al.
4	data analysis	Sparky	3.106	Goddard
5	refinement	X-PLOR	2.9.9	Brunger
6	refinement	NAMD	2.6b2	Schulten et al.