# OVERVIEW

BACK

The SAXS1 beamline is an experimental station dedicated to Small Angle X-ray Scattering (SAXS), operating at a fixed energy of 8 keV. It focuses on structural investigations of materials and biological samples, from the nanometer to a hundred nanometer scale, with applications in material science, chemistry, gels, rheology, structural biology, environmental and geosciences. Other experimental technique available includes Wide Angle X-ray Scattering (WAXS).

Due to the high photon flux, time-resolved SAXS can be performed reaching sub-second time-resolution for kinetic studies.

Several sample environment are made available to the user community, such as (1) furnaces (Linkam THMS600*) allowing temperatures from -200°C up to 600°C, (2) stretching devices (Linkam TST350), (3) circulating solution system with a peristaltic pump for in situ studies, (4) stopped-flow device (Biologic*), (5) autosampler (Spark Holland) for automatic loading of protein solutions.

(*) Multi-user equipments funded by FAPESP: Project 04/09447-9. PROEM – INSTRUMENTACAO DA LINHA SAXS2 DO LNLS: APLICACOES DA TECNICA DE SAXS AO ESTUDO DE MATERIAIS NANOESTRUTURADOS, POLIMEROS DENSOS E SISTEMAS BIOLÓGICOS

# CONTACT & STAFF

Beamline Phone Number: +55 19 3512 1132

Coordinator: Florian Edouard Pierre Meneau
Number: +55 19 3512 1132
E-mail: florian.meneau@lnls.br

# EXPERIMENTAL TECHNIQUES

The following experimental techniques and setups are available to users in this beamline. To learn more about the techniques’ limitations and requirements (sample, environment, etc.) contact the beamline coordinator before submitting your proposal.

• SMALL ANGLE X-RAY SCATTERING (SAXS)
• WIDE ANGLE X-RAY SCATTERING (WAXS)

# LAYOUT & OPTICAL ELEMENTS

ElementTypePosition[m]Description
SOURCEBending Magnet0.0Bending Magnet D01 exit B (15°), 1.67 T, 890$\mu \rm m$ x 150$\mu \rm m$ at 8 keV
S0Whitebeam Slits7.2
MonoToroidal Side-bounce Monochromator8.0W/B4C Multilayer (500 double layers) on Si substrate
S1Slits8,5-
S2Slits14.0-
S3Slits16.0-
DetectorPilatus 300K17.2-

# PARAMETERS

ParameterValueCondition
Energy range [keV]8Si(111)
Energy resolution [$\Delta$E/E]0.1Si(111)
Beam size at sample [$\rm mm^2$, FWHM]1.5 x 1at 8 keV
Flux density at sample [ph/s/$\rm mm^2$]$10^{10} - 10^{12}$-

# INSTRUMENTATION

InstrumentTypeModelSpecificationsManufacturer
Detector2DPilatus 300K172 $\mu \rm m$ pixel, 487 x 689 pixels, 200Hz frame rateDectris
Detector2DPilatus 100K172 $\mu \rm m$ pixel, 487 x 195 pixels, 200Hz frame rateDectris
AutosamplerAutomatic sample loading for biology-96 wells plateSpark Holland
Furnace *Transmission / Capillary / MicaDSC600Temp. Range: -196°C – 600°C, Max. Temp Rate: 30C/s, Solid and Liquid SamplesLinkam
Tensile Stretching StageTransmissionTST350Temp. Range: -150°C – 600°C, in-airLinkam
PALMITransmission / Mica- Liquid Samples, Thermal bath temp. control available, 300 $\mu \rm L$ minimum sample volume. LNLS in-house development
PASMITransmission-Solid Samples, 7 slots, motorizedLNLS in-house development
Capillary CellTransmission / Capillary-Liquid Samples, Thermal bath temp. control available, 80 $\mu \rm L$ minimum sample volume.LNLS in-house development
Biologic stopped-flow *TransmissionSFM400-BioLogic Science Instruments

# CONTROL AND DATA ACQUISITION

All beamline controls are done through EPICS (Experimental Physics and Industrial Control System), running on a PXI from National Instruments. The data acquisition is done using a Red Hat workstation with Python scripts, developed at LNLS with SOL group. CSS (Control System Studio) is used as a graphical interface to display and control the beamline devices.

# APPLYING FOR BEAMTIME

Submission calls are usually announced twice per year, one for each semester. All the academic research proposals must be submitted electronically through the SAU Online portal. Learn more about how to submit a proposal here.

It is recommended that new users contact the beamline group members for discussing the experimental proposal before submission.

# DOCUMENTATION

###### BEAMLINE MANUAL
• Click here to access a manual for the main commands of the beamline.

# HOW TO CITE THIS BEAMLINE

Users are required to acknowledge the use of LNLS facilities in any publications and to inform the Laboratory about any publications, thesis and other published materials. Users must also cooperate by supplying this information upon request.

Support text for acknowledgements:

This research used resources of the Brazilian Synchrotron Light Laboratory (LNLS), an open national facility operated by the Brazilian Centre for Research in Energy and Materials (CNPEM) for the Brazilian Ministry for Science, Technology, Innovations and Communications (MCTIC). The _ _ _ beamline staff is acknowledged for the assistance during the experiments.

# OTHER REFERENCES

Soren Skou, Richard E Gillilan and Nozomi Ando. Synchrotron-based small-angle X-ray scattering of proteins in solution.  Nature Protocols 9, 1727–1739 (2014). DOI:10.1038/nprot.2014.116

With recent advances in data analysis algorithms, X-ray detectors and synchrotron sources, small-angle X-ray scattering (SAXS) has become much more accessible to the structural biology community. Although limited to 10 Å resolution, SAXS can provide a wealth of structural information on biomolecules in solution and is compatible with a wide range of experimental conditions. SAXS is thus an attractive alternative when crystallography is not possible. Moreover, advanced use of SAXS can provide unique insight into biomolecular behavior that can only be observed in solution, such as large conformational changes and transient protein-protein interactions. Unlike crystal diffraction data, however, solution scattering data are subtle in appearance, highly sensitive to sample quality and experimental errors and easily misinterpreted. In addition, synchrotron beamlines that are dedicated to SAXS are often unfamiliar to the nonspecialist. Here we present a series of procedures that can be used for SAXS data collection and basic cross-checks designed to detect and avoid aggregation, concentration effects, radiation damage, buffer mismatch and other common problems. Human serum albumin (HSA) serves as a convenient and easily replicated example of just how subtle these problems can sometimes be, but also of how proper technique can yield pristine data even in problematic cases. Because typical data collection times at a synchrotron are only one to several days, we recommend that the sample purity, homogeneity and solubility be extensively optimized before the experiment.

V. Petoukhov, D. Franke, A. V. Shkumatov, G. Tria, A. G. Kikhney, M. Gajda, C. Gorba, H. D. T. Mertens, P. V. Konarev and D. I. Svergun. New developments in the ATSASprogram package for small-angle scattering data analysis. J. Appl. Cryst. (2012). 45, 342-350.DOI:10.1107/S0021889812007662

New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.

Michel H. J. Koch, Patrice Vachette and Dmitri I. Svergun. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution, Quarterly Reviews of Biophysics, 36(2), pp. 147–227 (2003). DOI: 10.1017/S0033583503003871

A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies – on ribosomes and on the allosteric protein aspartate transcarbamoylase – illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

Martel, P. Liu, T. M. Weiss, M. Niebuhr and H. Tsuruta. An integrated high-throughput data acquisition system for biological solution X-ray scattering studies. J. Synchrotron Rad. (2012). 19, 431-434. DOI: 10.1107/S0909049512008072

A fully automated high-throughput solution X-ray scattering data collection system has been developed for protein structure studies at beamline 4-2 of the Stanford Synchrotron Radiation Lightsource. It is composed of a thin-wall quartz capillary cell, a syringe needle assembly on an XYZ positioning arm for sample delivery, a water-cooled sample rack and a computer-controlled fluid dispenser. It is controlled by a specifically developed software component built into the standard beamline control program Blu-Ice/DCS. The integrated system is intuitive and very simple to use, and enables experimenters to customize data collection strategy in a timely fashion in concert with an automated data processing program. The system also allows spectrophotometric determination of protein concentration for each sample aliquot in the beam via an in situ UV absorption spectrometer. A single set of solution scattering measurements requires a 20-30 µl sample aliquot and takes typically 3.5 min, including an extensive capillary cleaning cycle. Over 98.5% of measurements are valid and free from artefacts commonly caused by air-bubble contamination. The sample changer, which is compact and light, facilitates effortless switching with other sample-handling devices required for other types of non-crystalline X-ray scattering experiments.

# PUBLICATIONS

Scientific publications produced with data obtained at the facilities of this beamline, and published in journals indexed by the Web of Science, are listed below.

Attention Users: Given the importance of the previous scientific results to the overall proposal evaluation process, users are strongly advised to check and update their publication record both at the SAU Online website and at the For the library, updates can be made by sending the full bibliographic data to the CNPEM library (biblioteca@cnpem.br). Publications are included in the database after being checked by the CNPEM librarians and the beamline coordinators.

MORE PUBLICATIONS

SAXS1

Tarutani, N.; Tokudome, Y.; Jobbágy, M.; Soler-Illia, G. J. A. A.; Tang, Q. ; Müller, M. ; Takahashi, M.. Highly Ordered Mesoporous Hydroxide Thin Films through Self-Assembly of Size-Tailored Nanobuilding Blocks: A Theoretical-Experimental Approach, Chemistry of Materials, v. 31, n. 2, p. 322-330, 2019. DOI: 10.1021/acs.chemmater.8b03082

SAXS1   SAXS2

Capeletti, L. B.; Santos, C. dos; Rocha, Z. N. da; Cardoso, M. B.; Santos, J. H. Z. dos. Chemically modified silica-based sensors: Effect of the nature of organosilane, Sensors and Actuators B-Chemical, v. 282, p. 798-808, 2019. DOI: 10.1016/j.snb.2018.10.137

SAXS1

Figueiredo, A. S. ; Icart, L. P. ; Marques, F. D.; Fernandes, E. R. ; Ferreira, L. P. ; Oliveira, G. E.; Souza Jr., F. G.. Extrinsically magnetic poly(butylene succinate): An up-and-coming petroleum cleanup tool, Science of the Total Environment, v. 647, p. 88-98, 2019. DOI: 10.1016/j.scitotenv.2018.07.421

SAXS1

Abreu, T. H.; Meyer, C. I.; Padró, C.; Martins, L.. Acidic V-MCM-41 catalysts for the liquid-phase ketalization of glycerol with acetone, Microporous and Mesoporous Materials, v. 273, p. 219-225, 2019. DOI: 10.1016/j.micromeso.2018.07.006

SAXS1

Veloso-Silva, V. L. W. ; Dores-Silva, P. R.; Bertolino-Reis, D. E. ; Moreno-Oliveira, L. F. ; Libardi, S. H.; Borges, J. C.. Structural studies of Old Yellow Enzyme of Leishmania braziliensis in solution, Archives of Biochemistry and Biophysics, v. 661, p. 87-96, 2019. DOI: 10.1016/j.abb.2018.11.009

SAXS1

Germiniani, L. G. L.; Silva, L. C. E.; Plivelic, T. S.; Gonçalves, M. C.. Poly(epsilon-caprolactone)/cellulose nanocrystal nanocomposite mechanical reinforcement and morphology: the role of nanocrystal pre-dispersion, Journal of Materials Science, v. 54, n. 1, p. 414-426, 2019. DOI: 10.1007/s10853-018-2860-9

MORE PUBLICATIONS