Model of rat Crry determined by solution scattering, curve fitting and homology modelling
SOLUTION SCATTERING
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
MSI
2000
1
THE MODELLED SCATTERING
CURVES WERE ASSESSED BY CALCULATION OF THE
RG AND RSX-1 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).
1
HOMOLOGY MODELS WERE BUILT FOR
THE 5 SCR DOMAINS AND ENERGY MINIMISATIONS WERE
PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL.
BIANTENNARY COMP ...
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.