Model of human IgA2 determined by solution scattering, curve fitting and homology modelling
SOLUTION SCATTERING
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 RELATIV ...
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.