BioXTAS RAW 2.0: the latest in SAXS data analysis

This chapter provides a detailed example of SAXS data analysis from a well behaving system. After collecting the SAXS data, several data analysis procedures are illustrated to ensure the data were of sufficient quality. Many of these steps are performed by comparing multiple concentrations from a dilution series, demonstrating the importance of this step in the data collection procedure for ensuring high quality data. Finally, real space modeling and shape reconstructions are shown to determine the oligomeric state as a tetramer, and identify the correct oligomeric assembly from crystal packing predictions.

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SAS-cam: a program for automatic processing and analysis of small-angle scattering data

Journal of Applied Crystallography ◽

10.1107/s1600576720008985 ◽

2020 ◽

Vol 53 (4) ◽

pp. 1147-1153 ◽

Cited By ~ 1

Author(s):

Hongjin Wu ◽

Yiwen Li ◽

Guangfeng Liu ◽

Haiguang Liu ◽

Na Li

Keyword(s):

Data Analysis ◽

High Throughput ◽

Small Angle ◽

Scattering Data ◽

Model Parameters ◽

Biological Macromolecules ◽

Shanghai Synchrotron Radiation Facility ◽

Saxs Data ◽

Model Interpretation ◽

Analysis Process

Small-angle X-ray scattering (SAXS) is a widely used method for investigating biological macromolecules in structural biology, providing information on macromolecular structures and dynamics in solution. Modern synchrotron SAXS beamlines are characterized as high-throughput, capable of collecting large volumes of data and thus demanding fast data processing for efficient beamline operations. This article presents a fully automated and high-throughput SAXS data analysis pipeline, SAS-cam, primarily based on the SASTBX package. Five modules are included in SAS-cam, encompassing the data analysis process from data reduction to model interpretation. The model parameters are extracted from SAXS profiles and stored in an HTML summary file, ready for online visualization using a web browser. SAS-cam can provide the user with the possibility of optimizing experimental parameters based on real-time feedback and it therefore significantly improves the efficiency of beam time. SAS-cam is installed on the BioSAXS beamline at the Shanghai Synchrotron Radiation Facility. The source code is available upon request.

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Structural insights into rice SalTol QTL located SALT protein

Scientific Reports ◽

10.1038/s41598-020-73517-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Navdeep Kaur ◽

Amin Sagar ◽

Pankaj Sharma ◽

Ashish ◽

Pratap Kumar Pati

Keyword(s):

Data Analysis ◽

Radius Of Gyration ◽

Relative Positioning ◽

Salt Stress Tolerance ◽

Saxs Data ◽

X Ray ◽

X Ray Crystallography ◽

X Ray Scattering ◽

Sugar Unit ◽

Structural Insights

Abstract Salinity is one of the major stresses affecting rice production worldwide, and various strategies are being employed to increase salt tolerance. Recently, there has been resurgence of interest to characterize SalTol QTL harbouring number of critical genes involved in conferring salt stress tolerance in rice. The present study reports the structure of SALT, a SalTol QTL encoded protein by X-ray crystallography (PDB ID: 5GVY; resolution 1.66 Å). Each SALT chain was bound to one mannose via 8 hydrogen bonds. Compared to previous structure reported for similar protein, our structure showed a buried surface area of 900 Å2 compared to only 240 Å2 for previous one. Small-angle X-ray scattering (SAXS) data analysis showed that the predominant solution shape of SALT protein in solution is also dimer characterized by a radius of gyration and maximum linear dimension of 2.1 and 6.5 nm, respectively. The SAXS profiles and modelling confirmed that the dimeric association and relative positioning in solution matched better with our crystal structure instead of previously reported structure. Together, structural/biophysical data analysis uphold a tight dimeric structure for SALT protein with one mannose bound to each protein, which remains novel to date, as previous structures indicated one sugar unit sandwiched loosely between two protein chains.

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