1R70

Model of human IgA2 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	x-ray	neutron
Radiation/Neutron Source	SRS BEAMLINE 2.1	ESRF BEAMLINE ID02	ISIS
Synchrotron	Y	Y	N
Beamline Type	2.1	ID02	PULSED NEUTRON
Detector Type	500-CHANNEL QUADRANT	FRELON CCD CAMERA	AREA (TIME-OF-FLIGHT)
Detector Manufacturer Details
Temperature (K)	288	288	288
pH	7.4	7.4	7.4
Numer of Time Frames Used	10	10
Protein Concentration Range (mg/mL)	2-15	0.55-1.12	2.0-3.0
Sample Buffer	DULBECCO PBS	DULBECCO PBS	PBS IN 99.9% D2O
Data Reduction Software	OTOKO	MULTICCD	COLLETTE
Guiner Mean Radius Of Gyration (nm)	5.17	5.18	5.03
Sigma Mean Radius Of Gyration	0.11	0.09	0.01
R(XS-1) Mean Cross Sectional Radii (nm)	2.39	2.47	2.21
R(XS-1) Sigma Mean Cross Sectional Radii	0.1	0.09	0.1
R(XS-2) Mean Cross Sectional Radii (nm)	1.37	1.47	1.04
R(XS-2) Sigma Mean Cross Sectional Radii	0.16	0.08	0.06
P(R) Protein Length (nm)	1	16	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, O, SCTPL7, GNOM	ACCELRYS		10000	1	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 (ESRF X-RAYS) AND 2.2 NM-1 (ISIS NEUTRONS).	1	HOMOLOGY MODELS WERE BUILT FOR THE IGA2 FAB AND FC FRAGMENTS STARTING FROM THE IGA1 MODEL (PDB ENTRY 1IGA). THE POSITIONS OF THE FAB FRAGMENTS RELATIVE TO THE FC FRAGMENT WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOM HINGE PEPTIDE STRUCTURES PRODUCED BY MOLECULAR DYNAMICS SIMULATIONS WITH CURVE-FITTING TO EXPERIMENTAL SOLUTION SCATTERING DATA. 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. A SINGLE ARRANGEMENT OF THE FAB FRAGMENTS IS PRESENTED, WHICH IS REPRESENTATIVE OF A FAMILY OF STRUCTURES THAT FIT THE SCATTERING DATA. MORE DETAILS ON THE MODELLING STRATEGY ARE CONTAINED IN THE PRIMARY REFERENCE.

Diffraction

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE		SRS
2	SYNCHROTRON	ESRF BEAMLINE ID2		ESRF	ID2
3	NUCLEAR REACTOR	ISIS INSTRUMENT LOQ