1NTL

Model of mouse Crry-Ig determined by solution scattering, curve fitting and homology modelling

SOLUTION SCATTERING

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Solution Scattering Data Acquistion	1	2	3
Scattering Type	x-ray	neutron	neutron
Radiation/Neutron Source	SRS BEAMLINE 2.1	ILL	ISIS
Synchrotron	Y	N	N
Beamline Type	2.1		PULSED NEUTRON
Detector Type	500-CHANNEL QUADRANT	AREA	AREA (TIME-OF-FLIGHT)
Detector Manufacturer Details
Temperature (K)	288	288	288
pH	7.5	7.5	7.5
Numer of Time Frames Used	10
Protein Concentration Range (mg/mL)	2-15	8.2	4.5-6.8
Sample Buffer	TRIS	PBS IN 99.9% D2O	PBS IN 99.9% D2O
Data Reduction Software	OTOKO	DETEC, RNILS, SPOLLY	COLLETTE
Guiner Mean Radius Of Gyration (nm)	5	4.9	4.9
Sigma Mean Radius Of Gyration	0.4	0.2	0.2
R(XS-1) Mean Cross Sectional Radii (nm)	1.5	1.2	1.2
R(XS-1) Sigma Mean Cross Sectional Radii	0.1	0.2	0.2
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)	1		1

Solution Scattering Data Analysis and Model Fitting
Method	Software	Software Authors	Starting Model	Conformers, Number Calculated	Conformers, Number Submitted	Conformers, Selection Criteria	Best Representative Conformer	Other Details
CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS	INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, SCTPL5, GNOM	MSI		2000	2	THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 2.2 NM-1 (X-RAYS) AND 1.12 NM-1 (ILL NEUTRONS). TWO MODELS ARE SUBMITTED. PLEASE SEE LEGENDS TO FIGURE 15(B) AND FIGURE 15(C) IN ASLAM ET AL. FOR AN EXPLANATION OF MODELS 1 AND 2 RESPECTIVELY.		HOMOLOGY MODELS WERE BUILT FOR THE 5 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. BIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES (MAN3GLCNAC4GAL2FUC0NEUNAC2) WERE ADDED TO EACH OF THE N-LINKED GLYCOSYLATION SITES. A LIBRARY OF LINKER PEPTIDE CONFORMATIONS WAS USED IN DOMAIN MODELLING CONSTRAINED BY THE SOLUTION SCATTERING FITS. MODELLING WITH THE SCATTERING DATA WAS ALSO CARRIED OUT BY ROTATIONAL SEARCH METHODS. THE X-RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED MODELS.

Diffraction

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE	1	SRS
2	NUCLEAR REACTOR	ILL BEAMLINE D11	10	ILL	D11
3	NUCLEAR REACTOR	ISIS INSTRUMENT LOQ	2-10