- Email: [email protected]
The small-angle X-ray scattering beamline BioMUR at the Kurchatov synchrotron radiation source
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Contents lists available at ScienceDirect
Nuclear Inst. and Methods in Physics Research, A journal homepage: www.elsevier.com/locate/nima
The small-angle X-ray scattering beamline BioMUR at the Kurchatov synchrotron radiation source G.S. Peters a ,∗, O.A. Zakharchenko a,b , P.V. Konarev a,c , Y.V. Karmazikov d , M.A. Smirnov d , A.V. Zabelin a , E.H. Mukhamedzhanov a , A.A. Veligzhanin a , A.E. Blagov a , M.V. Kovalchuk a,c a
National Research Centre ‘‘Kurchatov Institute’’, Akademika Kurchatova pl., 1, Moscow, 123182, Russian Federation M.V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119991, Russian Federation c A.V.Shubnikov Institute of Crystallography of Federal Scientific Research Centre, ‘‘Crystallography and Photonics’’ of Russian Academy of Sciences, Leninskii pr. 59, Moscow, 119333, Russian Federation d Private limited company ‘‘Russian Industrial Company’’, Akademika Kurchatova pl., 1, bldg. 5, Moscow, 123182, Russian Federation b
ARTICLE Keywords: Synchrotron radiation Synchrotron source X-ray Small-angle scattering Beamline
INFO
ABSTRACT A small-angle X-ray scattering beamline BioMUR has been constructed and is now in operation at the Kurchatov synchrotron radiation source (Moscow Russian Federation). Using X-ray optic elements and equipment of the former beamlines DICSY (Kurchatov source) and X33 (EMBL c/o DESY) Hamburg, Germany, BioMUR has been commissioned to deliver an optimized configuration that provides a significant improvement in the quality of small-angle scattering patterns at the Kurchatov synchrotron radiation source. It allows one to study a wide spectrum of samples at different conditions using the automated control software.
1. Introduction Small-angle X-ray scattering allows one to obtain information on nanoscale particle size and structure in solution. The method is popular in the biological and soft matter scientific communities and has been widely used at synchrotron radiation sources worldwide. In particular, one of the first SAXS beamlines was X33 at the DORIS storage ring (EMBL c/o DESY) [1]. Its logical continuation is the station P12 at the PETRA III storage ring [2]. At the European synchrotron radiation facility (ESRF), two small-angle X-ray beamlines are in operation — the BM29 beamline for standard SAXS experiments [3] and the undulator beamline ID02 for advanced experiments (e.g. those requiring ultralow angles). SAXS beamlines also operate in the UK (the B21 beamline at Diamond [4]), in Italy at Elettra [5] and at other synchrotrons worldwide. The SAXS method is very sensitive to the stability of the primary beam and the accuracy of the setup alignment. It is necessary to focus the synchrotron radiation (SR) beam, which is usually carried out by bending the monochromator and the mirror, and to provide robust collimation to reduce the background scattering, for example, using the Kratky three-slit scheme. Small-angle X-ray beamlines should be upgraded regularly to obtain the best data quality from optimized hardware. Small-angle X-ray scattering experiments at the Kurchatov synchrotron radiation source were previously carried out at the beamline DICSY [6], one of the first experimental beamlines established ∗
at the synchrotron. BioMUR, originally intended for powder diffraction, was upgraded to perform SAXS experiments following a number of technical improvements: replacement of the gas detector with a new photon-counting pixel detector (DECTRIS Pilatus3 1M) with an extended dynamic range, installation of a thermostabilized capillary holder, upgrade of the feedback system, and replacement of the vacuum system. Additional technical problems had to be solved to further improve experimental conditions, including: insufficiently low vacuum (10−3 bar), manual mechanical adjustment of the optical elements, the lack of automation of optics and experiment control, insufficient accuracy of the beam collimation, the inability of installing several samples for the experiment, and the use of non-standard scattering chambers that require expert handling to change. These problems could not be resolved without a major upgrade of the beamline. The following sections describe the main components and characteristics of the small-angle X-ray scattering beamline BioMUR, constructed using the elements of the DICSY/X33 beamlines, on which, from the beginning of 2018, users have the opportunity to perform SAXS experiments. 2. Experimental setup During the construction of the BioMUR beamline at the Kurchatov synchrotron radiation source the performance experience of the former DICSY beamline was taken into account and its functionality was
Corresponding author. E-mail address: [email protected] (G.S. Peters).
https://doi.org/10.1016/j.nima.2019.162616 Received 18 June 2019; Received in revised form 18 August 2019; Accepted 19 August 2019 Available online 22 August 2019 0168-9002/© 2019 Elsevier B.V. All rights reserved.
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Fig. 1. Scheme of the small-angle X-ray scattering beamline BioMUR.
expanded in order to implement the possibility of a wide spectrum of samples. The beamline has a typical setup (Fig. 1) with one focusing monochromator, one focusing mirror and the set of collimation slits. During the construction of the beamline, some of the equipment from the former SAXS beamline X33 (Hamburg, Germany) was used. The location of the beamline was chosen to maximize the distance from the radiation source (bending magnet in the storage ring) to the monochromator. At the beamline BioMUR this distance is 24.2 m, while at DICSY it was only 14 m. According to geometrical optics calculations, it is possible to achieve a beam focusing with the size that is now more than 1.5 times smaller in lateral dimensions than at the old station. The specifications of the BioMUR beamline are shown in Table 1, and the photo of the beamline, including the last block of slits and the sample-to-detector area, is shown in Fig. 2. Most of the significant technical limitations of the DICSY beamline were taken into account in the design of the BioMUR beamline. In particular, the list of improvements that were implemented in the BioMUR beamline include: high vacuum (10−5 –10−6 mbar), vacuum of the entire optical path from the source to the sample, motorized adjustment of optical elements, the standard TANGO-based automated control system (ACS), monitors of the beam position before and after the monochromator and in front of the sample chamber, automatically inserted attenuators for the initial setup and the evaluation of the geometric parameters of the beam, an accurate beam collimation by a system of 4 slits in vacuum, a new sample changer with the ability to load, measure and automatically change multiple samples, and precast scattering chambers that accommodate a standardized replacement procedure. The original purpose of the former X33 beamline was mainly in the standard measurement of liquid solutions of biological macromolecules (proteins, lipids, DNA-like structures, etc.) in the angular range corresponding to the scattering vector from 0.03 nm−1 to 6 nm−1 . These measurements are facilitated at the BioMUR beamline through the inclusion of a robotic sample changer connected to a vacuum cell. This equipment has been commissioned and demonstrates good performance and suitability for experiments focused on solutions of biological macromolecules. However, a number of synchrotron users require a more flexible sample environment that affords measurement of a much wider spectrum of samples, both by the expected characteristic size of molecules (there are requirements to measure the structures with the sizes from 0.1 to 200 nm), and by their type and aggregate condition (samples with varying density and gel-like samples, powders, solids, biological tissues in the native state, and fibers of different composition), for which the former beamline was not suitable. Therefore, it was decided to replace the sample to detector section from X33 with that already used at the DICSY beamline, and to modify this section to enable the implementation of an optimized time scheme for high-throughput; one of the main goals of this new beamline. New sample holders were designed and manufactured (Fig. 3) – similar
Fig. 2. Photo of the BioMUR beamline.
to the original structures of DICSY beamline, but with the possibility of measuring several samples without a manual change — up to 5 samples in a capillary holder and up to 10 samples in a holder for solid samples. A Julabo FP89-HL thermostat was also installed with a special operating fluid having a freezing point of −90 ◦ C and a boiling point of +200 ◦ C. This made it possible to measure samples in a wide temperature range from −50 ◦ C to + 150 ◦ C (corrected for heat losses). As a monochromator, a silicon crystal Si(111) of a triangular shape is used, installed vertically at a Bragg angle of 13.5 ◦ . A stepper motor for bending the crystal and thus focusing the beam in a horizontal direction is also installed. The beam energy after the monochromator is approximately 8 keV. The flat mirror with rhodium sputtering of large size (about 1 m) is used to capture the largest possible part of the beam after the monochromator. The mirror has a gravimetric bending mechanism for focusing the beam in the vertical direction. The mirror is also responsible for filtering out the third harmonic of the transmitted beam further towards the sample, which still has noticeable intensity after the monochromator (about 4% of the main harmonic). The beam is collimated by four slit sets in a vacuum design, two of which were initially located inside the mirror compartment, and two in the span from the mirror to the sample. During beamline commissioning it was observed that the first set of slits was not required for collimation (however, it can be used as an additional beam size filter), the second set of slits is used to limit the beam size and the effects associated with the secondary scattering on the remaining slit sets when measured at the lowest angles, the third and fourth sets, configured according to Kratky’s collimation scheme [8], serve to minimize the effects of the secondary scattering on the slit edges, since the slits themselves 2
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Table 1 The specifications of the BioMUR beamline. Light source Monochromator X-ray energy Energy bandwidth (𝛥E/E) [7] Mirror Photon flux at the sample Beam size at the sample Measurable q-range Detector
1.7 T bending magnet @ 2.5 GeV synchrotron, Ec = 7.1 keV Si(111) triangular crystal, max white beam aperture 4 × 10 mm, asymmetric cut 7◦ , bender for horizontal focusing 8 keV (𝜆 = 0.1445 nm) 5 × 10−3 Single, rhodium coated, length 1000 mm, bender for vertical focusing 1010 –1011 ph/s @ 100 mA (depends on collimation) 500 × 350 μm 0.03–30 nm−1 2D, DECTRIS Pilatus3 1M, 1043 × 981 pixels, 20 bit dynamic range, 500 Hz
Fig. 3. New holders — for capillary (a) and solid (b) samples.
are not made of a single crystal material. To observe the position and the shape of the beam at the beamline, there are two video cameras located after the monochromator and before the last set of slits. The first camera is equipped with a feedback system for transmitting data to the control panel and stabilizing the beam orbit. The second camera is equipped with a squeezing phosphor probe to assess the position of the beam coming through the optical path of the beamline and correct it if necessary. There is also a video camera with a reflector that directs the image from the sample holder to determine the position of the beam directly on the sample. In order to protect the samples from the X-ray exposure outside the exposure time, a pneumatic high-speed shutter is used, which is synchronized with the detector and is opened only for the duration of the exposure. As a detector, a 2D Pilatus3 1M system (DECTRIS, Switzerland) is used. This detector has high dynamic range of 20 bit and practically zero background noise, which allows registering very weak scattering signals at wide angles without reaching the intensity limit at small angles. Its high speed of taking images (up to 500 Hz) makes it possible to do time-resolved SAXS experiments. As a beamstop, to protect the detector from the direct beam, a simple circular piece of Pb is used. The size of the spot is 4 mm, and the thickness is 0,2 mm, which is enough to fully eliminate the incident beam. The beamstop is located on the exit window of the scattering chamber, when one uses the SAXS configuration (Fig. 4, a), or it is placed near the detector window on a special frame with manual adjustment in the WAXS case (Fig. 4, b). The original X33 design did not allow for changing the sample to detector distance, but included an option to install a second detector at the front of the scattering chambers (see Fig. 1) for data collection at wider angles. To facilitate adjustment of the sample to detector distance an aluminum guide beam with a length of 3.06 m was moved from the old DICSY beamline together with a moving table on which the detector was installed to BioMUR. Specialized steel tubes of a type-setting construction with the possibility of vacuuming (Fig. 5, a) were designed, manufactured and installed, allowing for a straightforward change of sample-to-detector distance across a wide range from 150 mm to 2500 mm (corresponding to a range of characteristic sample sizes from 0.2 to 200 nm) in 50 mm increments by adding or removing additional sections. These pipes are used as the new scattering chambers, with front and rear 15 μm mylar windows. To support the tube movement and to adjust the position of the beamstop, the special motorized shifts with a displacement range of 100 mm in the vertical direction and 30 mm in the horizontal direction
Fig. 4. Beamstop, SAXS (a) and WAXS (b) configuration.
were purchased (Fig. 5, b). The difference in ranges is chosen due to practical considerations. The sample assembly is also equipped with the motorized slides, however, for experimental purposes, the stroke in the horizontal direction is increased to 250 mm. The accuracy of the movements in all coordinates is within 10 μm. 3. Software The beamline contains a large number of electromechanical elements that ensure the mutual movement of the components of the X-ray optical path. For these purposes, the limit switches and lowering mechanisms are provided. A wide variety of engine types and parameters of transmission mechanisms required a unified and most convenient technical solution for the configuration. As the basis for building the system, the reliable multi-axis industrial controllers of MC4U stepping motors, manufactured by ACS, were chosen. The control system has a video segment, which is necessary to ensure the monitoring of the individual parts of the beamline, the location of the beam on the phosphor screens and the operation of the beam stabilization system. The integration of an analog video signal is performed using an analog video signal encoder into a video stream. 3
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Fig. 5. Typesetting pipes for evacuating the sample–detector distance (a), stepper motor assembly for typesetting pipes (b).
Fig. 6. The topology of the video subsystem.
Fig. 7. Graphical interface of the beamline control system.
The topology of the video subsystem shown in Fig. 6 indicates the location of the components. The diverse range of scientific tasks being solved at the beamline, in turn, demanded a high flexibility of the control system and the possibility of its adjustment for the experiments. According to the results of a review of existing approaches to the construction of similar systems on other synchrotrons, the TANGO software platform was identified as the de facto standard for building automation systems for scientific equipment at synchrotron sources worldwide. This platform provides modularity, abstraction and unification of the interface of hardware
components. For the platform in free access there is a significant number of so-called ‘‘tango servers’’, which are software packages that hide the details of the implementation of interactions with the device and provide a relatively standard interface to higher levels, similar to the devices of the same class (for example, for engines). To build a graphical interface of the system, the Taurus package [9] was used, which is widely used to manage TANGO systems. To manage the elements of the beamline, the special software and graphical interfaces were developed (Figs. 7–8). 4
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Fig. 8. Graphical window for the monochromator control.
Fig. 9. The distribution of beam (a) in horizontal (b) and vertical (c) coordinate.
4. Beamline commissioning
the capillary and solid-state holder, respectively, due to the automatic movement of the cell without opening the experimental hutch; the angular range is increased in one position of the detector by 1.5 times; the detector defects associated with the technical design of the setup (the shadow from the holder, windows, etc.) are significantly reduced. To illustrate the observed improvements, the scattering curves (after background subtraction) from bovine serum albumin obtained at the DICSY and BioMUR beamlines are shown (Fig. 10). Normalization of samples and buffers was carried out by dividing the recorded scattering intensities by the synchrotron current (in mA) and multiplying by 100 mA (as the standard current value). Verification of this normalization can be done by checking the intensity of calculated curve at larger angles (which tends to zero due to the significantly lower scattering). As the current sample environment for high viscosity and gel-like samples is not in vacuum, there remains an air gap around the sample, and thus it is impossible to completely eliminate the appearance of some defects in the recorded scattering data. Due to the difference in absorption of radiation scattered by the sample holder, there are corresponding shadows or highlights in the final image. However, in most cases, a potentially useful (‘‘clean’’) area in a two-dimensional picture from a detector, suitable for integration and further processing, has been expanded significantly. An example of a 2D image from the detector is shown in Fig. 11. Experiments in a vacuum cell are technically possible at this beamline in the case of using the cell from the X33 beamline connected with a robotic sample changer [11], however, the variety of samples suitable for this cell is limited to liquids with a low viscosity. To reduce the contribution of the instrumental background to the recorded scattering patterns the systematic elimination of possible
The size of the focused beam on the detector (pixel size 172×172 μm) was measured to verify the compliance with theoretical calculations. To avoid damaging the detector with the direct beam, an attenuator was installed — an aluminum plate with a thickness of 1200 μm. Measurements of the beam width at half maximum (FWHM) (Fig. 9) yield 3 pixels (∼500 μm) on the horizontal coordinate and 2 pixels (∼350 μm) on the vertical coordinate, confirming the significant improvement in beam focusing compared to the previous set-up at DICSY (750×500 μm). After the image was focused on the beam detector, a beamstop was installed and measurements of a calibration diffraction standard (silver behenate powder) were made to determine the X-ray wavelength. The processing of the experiment assumed a known sample–detector distance, measured with an accuracy of 1 mm. The diffraction pattern of silver behenate was radially averaged using the program Fit2D [10]. At the same time, the wavelength values were inserted into the program, starting from Cu–K𝛼 (0.154 nm), and the obtained sample–detector distance value was compared with the measured one. Then the procedure was repeated with the adjustment of the wavelength in the appropriate direction until the discrepancy with the experimental value was less than 1 mm. The final value of the wavelength was estimated as of 0.1445 nm. The first experiments at the beamline BioMUR showed a significant improvement of the data quality compared to the beamline DICSY: the signal-to-noise ratio increased by 3 times at exposures from 60 to 600 s; the transmitted intensity on the same control sample and the exposure time is decreased by 1.7 times; the period of continuous (noninterrupting) sample measurement is increased by 5 and 10 times for 5
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Fig. 10. Small-angle X-ray scattering curves of bovine serum albumin, measured at DICSY (blue) and BioMUR (red). Exposure time is 180 s, protein concentration is equal to 20 mg/ml. I is the intensity of the scattering of the sample, I0 is the intensity of the scattering of the buffer solution and q is the scattering vector. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 12. Comparison of the SAXS intensity of the various materials of the exit window. The exposure time is 180 s. Be1 and Be2 are the beryllium windows of the same thickness, but from two different manufacturers.
and 15 μm mylar window showed approximately 5 times weaker peak intensity (not concerning some slit scattering effects near the beamstop) than 70 μm window. The kapton window gave even lower scattering intensity at low angles, despite its larger thickness, but it turned out to be unsuitable for the experiment due to the presence of a diffraction maximum at wide angles (about 4 nm−1 , which is also shown, for example, in [12]). Thus, it was decided to replace the exit window material from beryllium to mylar of 15 μm thickness, which is the same material used in the front and rear windows of the scattering chamber. After replacement of the exit window, the quality of the low angle range of experimental data improved significantly. 5. Conclusions The goal of the construction of the beamline BioMUR was to improve the quality of SAXS experiments at the Kurchatov SR source through the replacement of outdated equipment. The beamline was built on a new, longer SR output channel, compared to the former SAXS beamline DICSY, and all components of the old beamline were replaced, partly using elements from the X33 beamline (EMBL c/o DESY). As a result, a better beam stability, with improved dimensions ∼ 500×350 μm at the detector was achieved. The average exposure time of the sample was decreased and the automated measurement of sets of biological samples achieved. The beamline set-up and tuning/adjustment time was significantly reduced due to the implementation of an automated control system based on Tango. Moreover, combined with the use of the powerful and efficient hybrid photon-counting pixel two-dimensional Pilatus3 1M detector (DECTRIS, Switzerland), the data quality is now comparable to that obtained at modern European SAXS beamlines. Since January of 2018, the beamline is in user operation [13], SAXS applications can be submitted through the website of the Kurchatov Institute (http://users.kcsni.nrcki.ru).
Fig. 11. Raw 2D image from BSA in 1,5 mm capillary. Sample-to-detector distance is 700 mm.
sources of scattering was conducted and windows on vacuum diaphragm tubes replaced. It was found that a major contribution to the background scattering intensity was the beryllium exit window located after the last set of slits and the beam shutter. This window divides the high vacuum and the atmosphere. To identify a more suitable replacement material for this window, comparative measurements of various materials for the exit window were carried out. The results are shown in Fig. 12. As can be seen from Fig. 12, the beryllium window makes a dramatic contribution to the low-angle scattering part of the scattering curve, which is more than 50,000 higher in relative units at the maximum compared to the signal from the air (in the absence of the sample). At the same time, the window from mylar gave a peak intensity of an order of magnitude less than the one from beryllium,
Acknowledgments We are grateful to Dr. D.I. Svergun and Dr. D. Franke (EMBL c/o DESY, Hamburg, Germany) for help in providing manuals for the elements of the former X33 beamline, Dr. V.V. Volkov (Institute of Crystallography, Moscow, Russia) for fruitful consultations on the beamline setup, Dr. A.Yu. Gruzinov (former member of our group, currently working at EMBL c/o DESY) for taking part in the TR&D of BIOMUR beamline and Dr. H.D.T. Mertens (EMBL c/o DESY, Hamburg, Germany) for his help in preparing the manuscript. The SAXS beamline BioMUR is a part of the unique scientific facility Kurchatov Synchrotron Radiation Source supported by the Ministry 6
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
of Education and Science of the Russian Federation (project code RFMEFI61917X0007). The study was supported by RFBR according to the research project №18-32-00885 mol_a and by the Ministry of Science and Higher Education within the State assignment FSRC ‘‘Crystallography and Photonics’’ of Russian Academy of Sciences (RAS).
[6] V.N. Korneev, et al., Nova versi malouglovo˘ i rentgenovsko˘ i apparatury dl issledovani biologiqeskih struktur na stancii diksi v kcsi i nt, Poverhnost~. Rentgenovskie, sinhrotronnye i ne˘ itronnye issledovani vol. 12, 2008, pp. 61–68. [7] H. Tajiri, H. Yamazaki, H. Ohashi, S. Goto, O. Sakata, T. Ishikawa, A middle energy-bandwidth X-ray monochromator for high-flux synchrotron diffraction: revisiting asymmetrically cut silicon crystals, J. Synchrotron Radiat. 26 (3) (2019) 750–755. [8] O. Glatter, O. Kratky, Small Angle X-Ray Scattering, Academic press, 1982. [9] C. Pascual-Izarra, et al., Effortless creation of control & data acquisition graphical user interfaces with Taurus, in: 15th International Conference on Accelerator and Large Experimental Physics Control Systems, ICALEPCS 2015. Conference Proceedings, 2015. [10] A.P. Hammersley, FIT2D: a multi-purpose data reduction, analysis and visualization program, J. Appl. Crystallogr. (2016). [11] A.R. Round, et al., Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33, J. Appl. Crystallogr. (2008). [12] H. Masunaga, K. Sakurai, I. Akiba, K. Ito, M. Takata, Accurate measurements of intrinsic scattering from window materials by use of a vacuum camera, J. Appl. Crystallogr. 46 (2) (2013) 577–579. [13] M.V. Kovalchuk, et al., Investigation of the structure of crystal-forming solutions of potassium dihydrogen phosphate K(H2PO4) (KDP type) on the basis of modeling precursor clusters and according to small-angle X-ray scattering data, Crystallogr. Rep. 64 (1) (2019) 6–10.
References [1] M.W. Roessle, et al., Upgrade of the small-angle X-ray scattering beamline x33 at the European Molecular Biology Laboratory, Hamburg, J. Appl. Crystallogr. (2007). [2] M.A. Graewert, et al., Automated pipeline for purification, biophysical and X-ray analysis of biomacromolecular solutions, Sci. Rep. (2015). [3] P. Pernot, et al., Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution, J. Synchrotron Radiat. (2013). [4] K. Inoue, J. Doutch, N. Terrill, The Current Status of Small-Angle X-Ray Scattering Beamline At Diamond Light Source, BUNSEKI KAGAKU, 2013. [5] H. Amenitsch, M. Rappolt, M. Kriechbaum, H. Mio, P. Laggner, S. Bernstorff, First performance assessment of the small-angle X-ray scattering beamline at ELETTRA, J. Synchrotron Radiat. (1998).
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Contents lists available at ScienceDirect
Nuclear Inst. and Methods in Physics Research, A journal homepage: www.elsevier.com/locate/nima
The small-angle X-ray scattering beamline BioMUR at the Kurchatov synchrotron radiation source G.S. Peters a ,∗, O.A. Zakharchenko a,b , P.V. Konarev a,c , Y.V. Karmazikov d , M.A. Smirnov d , A.V. Zabelin a , E.H. Mukhamedzhanov a , A.A. Veligzhanin a , A.E. Blagov a , M.V. Kovalchuk a,c a
National Research Centre ‘‘Kurchatov Institute’’, Akademika Kurchatova pl., 1, Moscow, 123182, Russian Federation M.V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119991, Russian Federation c A.V.Shubnikov Institute of Crystallography of Federal Scientific Research Centre, ‘‘Crystallography and Photonics’’ of Russian Academy of Sciences, Leninskii pr. 59, Moscow, 119333, Russian Federation d Private limited company ‘‘Russian Industrial Company’’, Akademika Kurchatova pl., 1, bldg. 5, Moscow, 123182, Russian Federation b
ARTICLE Keywords: Synchrotron radiation Synchrotron source X-ray Small-angle scattering Beamline
INFO
ABSTRACT A small-angle X-ray scattering beamline BioMUR has been constructed and is now in operation at the Kurchatov synchrotron radiation source (Moscow Russian Federation). Using X-ray optic elements and equipment of the former beamlines DICSY (Kurchatov source) and X33 (EMBL c/o DESY) Hamburg, Germany, BioMUR has been commissioned to deliver an optimized configuration that provides a significant improvement in the quality of small-angle scattering patterns at the Kurchatov synchrotron radiation source. It allows one to study a wide spectrum of samples at different conditions using the automated control software.
1. Introduction Small-angle X-ray scattering allows one to obtain information on nanoscale particle size and structure in solution. The method is popular in the biological and soft matter scientific communities and has been widely used at synchrotron radiation sources worldwide. In particular, one of the first SAXS beamlines was X33 at the DORIS storage ring (EMBL c/o DESY) [1]. Its logical continuation is the station P12 at the PETRA III storage ring [2]. At the European synchrotron radiation facility (ESRF), two small-angle X-ray beamlines are in operation — the BM29 beamline for standard SAXS experiments [3] and the undulator beamline ID02 for advanced experiments (e.g. those requiring ultralow angles). SAXS beamlines also operate in the UK (the B21 beamline at Diamond [4]), in Italy at Elettra [5] and at other synchrotrons worldwide. The SAXS method is very sensitive to the stability of the primary beam and the accuracy of the setup alignment. It is necessary to focus the synchrotron radiation (SR) beam, which is usually carried out by bending the monochromator and the mirror, and to provide robust collimation to reduce the background scattering, for example, using the Kratky three-slit scheme. Small-angle X-ray beamlines should be upgraded regularly to obtain the best data quality from optimized hardware. Small-angle X-ray scattering experiments at the Kurchatov synchrotron radiation source were previously carried out at the beamline DICSY [6], one of the first experimental beamlines established ∗
at the synchrotron. BioMUR, originally intended for powder diffraction, was upgraded to perform SAXS experiments following a number of technical improvements: replacement of the gas detector with a new photon-counting pixel detector (DECTRIS Pilatus3 1M) with an extended dynamic range, installation of a thermostabilized capillary holder, upgrade of the feedback system, and replacement of the vacuum system. Additional technical problems had to be solved to further improve experimental conditions, including: insufficiently low vacuum (10−3 bar), manual mechanical adjustment of the optical elements, the lack of automation of optics and experiment control, insufficient accuracy of the beam collimation, the inability of installing several samples for the experiment, and the use of non-standard scattering chambers that require expert handling to change. These problems could not be resolved without a major upgrade of the beamline. The following sections describe the main components and characteristics of the small-angle X-ray scattering beamline BioMUR, constructed using the elements of the DICSY/X33 beamlines, on which, from the beginning of 2018, users have the opportunity to perform SAXS experiments. 2. Experimental setup During the construction of the BioMUR beamline at the Kurchatov synchrotron radiation source the performance experience of the former DICSY beamline was taken into account and its functionality was
Corresponding author. E-mail address: [email protected] (G.S. Peters).
https://doi.org/10.1016/j.nima.2019.162616 Received 18 June 2019; Received in revised form 18 August 2019; Accepted 19 August 2019 Available online 22 August 2019 0168-9002/© 2019 Elsevier B.V. All rights reserved.
G.S. Peters, O.A. Zakharchenko, P.V. Konarev et al.
Nuclear Inst. and Methods in Physics Research, A 945 (2019) 162616
Fig. 1. Scheme of the small-angle X-ray scattering beamline BioMUR.
expanded in order to implement the possibility of a wide spectrum of samples. The beamline has a typical setup (Fig. 1) with one focusing monochromator, one focusing mirror and the set of collimation slits. During the construction of the beamline, some of the equipment from the former SAXS beamline X33 (Hamburg, Germany) was used. The location of the beamline was chosen to maximize the distance from the radiation source (bending magnet in the storage ring) to the monochromator. At the beamline BioMUR this distance is 24.2 m, while at DICSY it was only 14 m. According to geometrical optics calculations, it is possible to achieve a beam focusing with the size that is now more than 1.5 times smaller in lateral dimensions than at the old station. The specifications of the BioMUR beamline are shown in Table 1, and the photo of the beamline, including the last block of slits and the sample-to-detector area, is shown in Fig. 2. Most of the significant technical limitations of the DICSY beamline were taken into account in the design of the BioMUR beamline. In particular, the list of improvements that were implemented in the BioMUR beamline include: high vacuum (10−5 –10−6 mbar), vacuum of the entire optical path from the source to the sample, motorized adjustment of optical elements, the standard TANGO-based automated control system (ACS), monitors of the beam position before and after the monochromator and in front of the sample chamber, automatically inserted attenuators for the initial setup and the evaluation of the geometric parameters of the beam, an accurate beam collimation by a system of 4 slits in vacuum, a new sample changer with the ability to load, measure and automatically change multiple samples, and precast scattering chambers that accommodate a standardized replacement procedure. The original purpose of the former X33 beamline was mainly in the standard measurement of liquid solutions of biological macromolecules (proteins, lipids, DNA-like structures, etc.) in the angular range corresponding to the scattering vector from 0.03 nm−1 to 6 nm−1 . These measurements are facilitated at the BioMUR beamline through the inclusion of a robotic sample changer connected to a vacuum cell. This equipment has been commissioned and demonstrates good performance and suitability for experiments focused on solutions of biological macromolecules. However, a number of synchrotron users require a more flexible sample environment that affords measurement of a much wider spectrum of samples, both by the expected characteristic size of molecules (there are requirements to measure the structures with the sizes from 0.1 to 200 nm), and by their type and aggregate condition (samples with varying density and gel-like samples, powders, solids, biological tissues in the native state, and fibers of different composition), for which the former beamline was not suitable. Therefore, it was decided to replace the sample to detector section from X33 with that already used at the DICSY beamline, and to modify this section to enable the implementation of an optimized time scheme for high-throughput; one of the main goals of this new beamline. New sample holders were designed and manufactured (Fig. 3) – similar
Fig. 2. Photo of the BioMUR beamline.
to the original structures of DICSY beamline, but with the possibility of measuring several samples without a manual change — up to 5 samples in a capillary holder and up to 10 samples in a holder for solid samples. A Julabo FP89-HL thermostat was also installed with a special operating fluid having a freezing point of −90 ◦ C and a boiling point of +200 ◦ C. This made it possible to measure samples in a wide temperature range from −50 ◦ C to + 150 ◦ C (corrected for heat losses). As a monochromator, a silicon crystal Si(111) of a triangular shape is used, installed vertically at a Bragg angle of 13.5 ◦ . A stepper motor for bending the crystal and thus focusing the beam in a horizontal direction is also installed. The beam energy after the monochromator is approximately 8 keV. The flat mirror with rhodium sputtering of large size (about 1 m) is used to capture the largest possible part of the beam after the monochromator. The mirror has a gravimetric bending mechanism for focusing the beam in the vertical direction. The mirror is also responsible for filtering out the third harmonic of the transmitted beam further towards the sample, which still has noticeable intensity after the monochromator (about 4% of the main harmonic). The beam is collimated by four slit sets in a vacuum design, two of which were initially located inside the mirror compartment, and two in the span from the mirror to the sample. During beamline commissioning it was observed that the first set of slits was not required for collimation (however, it can be used as an additional beam size filter), the second set of slits is used to limit the beam size and the effects associated with the secondary scattering on the remaining slit sets when measured at the lowest angles, the third and fourth sets, configured according to Kratky’s collimation scheme [8], serve to minimize the effects of the secondary scattering on the slit edges, since the slits themselves 2
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Table 1 The specifications of the BioMUR beamline. Light source Monochromator X-ray energy Energy bandwidth (𝛥E/E) [7] Mirror Photon flux at the sample Beam size at the sample Measurable q-range Detector
1.7 T bending magnet @ 2.5 GeV synchrotron, Ec = 7.1 keV Si(111) triangular crystal, max white beam aperture 4 × 10 mm, asymmetric cut 7◦ , bender for horizontal focusing 8 keV (𝜆 = 0.1445 nm) 5 × 10−3 Single, rhodium coated, length 1000 mm, bender for vertical focusing 1010 –1011 ph/s @ 100 mA (depends on collimation) 500 × 350 μm 0.03–30 nm−1 2D, DECTRIS Pilatus3 1M, 1043 × 981 pixels, 20 bit dynamic range, 500 Hz
Fig. 3. New holders — for capillary (a) and solid (b) samples.
are not made of a single crystal material. To observe the position and the shape of the beam at the beamline, there are two video cameras located after the monochromator and before the last set of slits. The first camera is equipped with a feedback system for transmitting data to the control panel and stabilizing the beam orbit. The second camera is equipped with a squeezing phosphor probe to assess the position of the beam coming through the optical path of the beamline and correct it if necessary. There is also a video camera with a reflector that directs the image from the sample holder to determine the position of the beam directly on the sample. In order to protect the samples from the X-ray exposure outside the exposure time, a pneumatic high-speed shutter is used, which is synchronized with the detector and is opened only for the duration of the exposure. As a detector, a 2D Pilatus3 1M system (DECTRIS, Switzerland) is used. This detector has high dynamic range of 20 bit and practically zero background noise, which allows registering very weak scattering signals at wide angles without reaching the intensity limit at small angles. Its high speed of taking images (up to 500 Hz) makes it possible to do time-resolved SAXS experiments. As a beamstop, to protect the detector from the direct beam, a simple circular piece of Pb is used. The size of the spot is 4 mm, and the thickness is 0,2 mm, which is enough to fully eliminate the incident beam. The beamstop is located on the exit window of the scattering chamber, when one uses the SAXS configuration (Fig. 4, a), or it is placed near the detector window on a special frame with manual adjustment in the WAXS case (Fig. 4, b). The original X33 design did not allow for changing the sample to detector distance, but included an option to install a second detector at the front of the scattering chambers (see Fig. 1) for data collection at wider angles. To facilitate adjustment of the sample to detector distance an aluminum guide beam with a length of 3.06 m was moved from the old DICSY beamline together with a moving table on which the detector was installed to BioMUR. Specialized steel tubes of a type-setting construction with the possibility of vacuuming (Fig. 5, a) were designed, manufactured and installed, allowing for a straightforward change of sample-to-detector distance across a wide range from 150 mm to 2500 mm (corresponding to a range of characteristic sample sizes from 0.2 to 200 nm) in 50 mm increments by adding or removing additional sections. These pipes are used as the new scattering chambers, with front and rear 15 μm mylar windows. To support the tube movement and to adjust the position of the beamstop, the special motorized shifts with a displacement range of 100 mm in the vertical direction and 30 mm in the horizontal direction
Fig. 4. Beamstop, SAXS (a) and WAXS (b) configuration.
were purchased (Fig. 5, b). The difference in ranges is chosen due to practical considerations. The sample assembly is also equipped with the motorized slides, however, for experimental purposes, the stroke in the horizontal direction is increased to 250 mm. The accuracy of the movements in all coordinates is within 10 μm. 3. Software The beamline contains a large number of electromechanical elements that ensure the mutual movement of the components of the X-ray optical path. For these purposes, the limit switches and lowering mechanisms are provided. A wide variety of engine types and parameters of transmission mechanisms required a unified and most convenient technical solution for the configuration. As the basis for building the system, the reliable multi-axis industrial controllers of MC4U stepping motors, manufactured by ACS, were chosen. The control system has a video segment, which is necessary to ensure the monitoring of the individual parts of the beamline, the location of the beam on the phosphor screens and the operation of the beam stabilization system. The integration of an analog video signal is performed using an analog video signal encoder into a video stream. 3
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Fig. 5. Typesetting pipes for evacuating the sample–detector distance (a), stepper motor assembly for typesetting pipes (b).
Fig. 6. The topology of the video subsystem.
Fig. 7. Graphical interface of the beamline control system.
The topology of the video subsystem shown in Fig. 6 indicates the location of the components. The diverse range of scientific tasks being solved at the beamline, in turn, demanded a high flexibility of the control system and the possibility of its adjustment for the experiments. According to the results of a review of existing approaches to the construction of similar systems on other synchrotrons, the TANGO software platform was identified as the de facto standard for building automation systems for scientific equipment at synchrotron sources worldwide. This platform provides modularity, abstraction and unification of the interface of hardware
components. For the platform in free access there is a significant number of so-called ‘‘tango servers’’, which are software packages that hide the details of the implementation of interactions with the device and provide a relatively standard interface to higher levels, similar to the devices of the same class (for example, for engines). To build a graphical interface of the system, the Taurus package [9] was used, which is widely used to manage TANGO systems. To manage the elements of the beamline, the special software and graphical interfaces were developed (Figs. 7–8). 4
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Fig. 8. Graphical window for the monochromator control.
Fig. 9. The distribution of beam (a) in horizontal (b) and vertical (c) coordinate.
4. Beamline commissioning
the capillary and solid-state holder, respectively, due to the automatic movement of the cell without opening the experimental hutch; the angular range is increased in one position of the detector by 1.5 times; the detector defects associated with the technical design of the setup (the shadow from the holder, windows, etc.) are significantly reduced. To illustrate the observed improvements, the scattering curves (after background subtraction) from bovine serum albumin obtained at the DICSY and BioMUR beamlines are shown (Fig. 10). Normalization of samples and buffers was carried out by dividing the recorded scattering intensities by the synchrotron current (in mA) and multiplying by 100 mA (as the standard current value). Verification of this normalization can be done by checking the intensity of calculated curve at larger angles (which tends to zero due to the significantly lower scattering). As the current sample environment for high viscosity and gel-like samples is not in vacuum, there remains an air gap around the sample, and thus it is impossible to completely eliminate the appearance of some defects in the recorded scattering data. Due to the difference in absorption of radiation scattered by the sample holder, there are corresponding shadows or highlights in the final image. However, in most cases, a potentially useful (‘‘clean’’) area in a two-dimensional picture from a detector, suitable for integration and further processing, has been expanded significantly. An example of a 2D image from the detector is shown in Fig. 11. Experiments in a vacuum cell are technically possible at this beamline in the case of using the cell from the X33 beamline connected with a robotic sample changer [11], however, the variety of samples suitable for this cell is limited to liquids with a low viscosity. To reduce the contribution of the instrumental background to the recorded scattering patterns the systematic elimination of possible
The size of the focused beam on the detector (pixel size 172×172 μm) was measured to verify the compliance with theoretical calculations. To avoid damaging the detector with the direct beam, an attenuator was installed — an aluminum plate with a thickness of 1200 μm. Measurements of the beam width at half maximum (FWHM) (Fig. 9) yield 3 pixels (∼500 μm) on the horizontal coordinate and 2 pixels (∼350 μm) on the vertical coordinate, confirming the significant improvement in beam focusing compared to the previous set-up at DICSY (750×500 μm). After the image was focused on the beam detector, a beamstop was installed and measurements of a calibration diffraction standard (silver behenate powder) were made to determine the X-ray wavelength. The processing of the experiment assumed a known sample–detector distance, measured with an accuracy of 1 mm. The diffraction pattern of silver behenate was radially averaged using the program Fit2D [10]. At the same time, the wavelength values were inserted into the program, starting from Cu–K𝛼 (0.154 nm), and the obtained sample–detector distance value was compared with the measured one. Then the procedure was repeated with the adjustment of the wavelength in the appropriate direction until the discrepancy with the experimental value was less than 1 mm. The final value of the wavelength was estimated as of 0.1445 nm. The first experiments at the beamline BioMUR showed a significant improvement of the data quality compared to the beamline DICSY: the signal-to-noise ratio increased by 3 times at exposures from 60 to 600 s; the transmitted intensity on the same control sample and the exposure time is decreased by 1.7 times; the period of continuous (noninterrupting) sample measurement is increased by 5 and 10 times for 5
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Fig. 10. Small-angle X-ray scattering curves of bovine serum albumin, measured at DICSY (blue) and BioMUR (red). Exposure time is 180 s, protein concentration is equal to 20 mg/ml. I is the intensity of the scattering of the sample, I0 is the intensity of the scattering of the buffer solution and q is the scattering vector. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 12. Comparison of the SAXS intensity of the various materials of the exit window. The exposure time is 180 s. Be1 and Be2 are the beryllium windows of the same thickness, but from two different manufacturers.
and 15 μm mylar window showed approximately 5 times weaker peak intensity (not concerning some slit scattering effects near the beamstop) than 70 μm window. The kapton window gave even lower scattering intensity at low angles, despite its larger thickness, but it turned out to be unsuitable for the experiment due to the presence of a diffraction maximum at wide angles (about 4 nm−1 , which is also shown, for example, in [12]). Thus, it was decided to replace the exit window material from beryllium to mylar of 15 μm thickness, which is the same material used in the front and rear windows of the scattering chamber. After replacement of the exit window, the quality of the low angle range of experimental data improved significantly. 5. Conclusions The goal of the construction of the beamline BioMUR was to improve the quality of SAXS experiments at the Kurchatov SR source through the replacement of outdated equipment. The beamline was built on a new, longer SR output channel, compared to the former SAXS beamline DICSY, and all components of the old beamline were replaced, partly using elements from the X33 beamline (EMBL c/o DESY). As a result, a better beam stability, with improved dimensions ∼ 500×350 μm at the detector was achieved. The average exposure time of the sample was decreased and the automated measurement of sets of biological samples achieved. The beamline set-up and tuning/adjustment time was significantly reduced due to the implementation of an automated control system based on Tango. Moreover, combined with the use of the powerful and efficient hybrid photon-counting pixel two-dimensional Pilatus3 1M detector (DECTRIS, Switzerland), the data quality is now comparable to that obtained at modern European SAXS beamlines. Since January of 2018, the beamline is in user operation [13], SAXS applications can be submitted through the website of the Kurchatov Institute (http://users.kcsni.nrcki.ru).
Fig. 11. Raw 2D image from BSA in 1,5 mm capillary. Sample-to-detector distance is 700 mm.
sources of scattering was conducted and windows on vacuum diaphragm tubes replaced. It was found that a major contribution to the background scattering intensity was the beryllium exit window located after the last set of slits and the beam shutter. This window divides the high vacuum and the atmosphere. To identify a more suitable replacement material for this window, comparative measurements of various materials for the exit window were carried out. The results are shown in Fig. 12. As can be seen from Fig. 12, the beryllium window makes a dramatic contribution to the low-angle scattering part of the scattering curve, which is more than 50,000 higher in relative units at the maximum compared to the signal from the air (in the absence of the sample). At the same time, the window from mylar gave a peak intensity of an order of magnitude less than the one from beryllium,
Acknowledgments We are grateful to Dr. D.I. Svergun and Dr. D. Franke (EMBL c/o DESY, Hamburg, Germany) for help in providing manuals for the elements of the former X33 beamline, Dr. V.V. Volkov (Institute of Crystallography, Moscow, Russia) for fruitful consultations on the beamline setup, Dr. A.Yu. Gruzinov (former member of our group, currently working at EMBL c/o DESY) for taking part in the TR&D of BIOMUR beamline and Dr. H.D.T. Mertens (EMBL c/o DESY, Hamburg, Germany) for his help in preparing the manuscript. The SAXS beamline BioMUR is a part of the unique scientific facility Kurchatov Synchrotron Radiation Source supported by the Ministry 6
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of Education and Science of the Russian Federation (project code RFMEFI61917X0007). The study was supported by RFBR according to the research project №18-32-00885 mol_a and by the Ministry of Science and Higher Education within the State assignment FSRC ‘‘Crystallography and Photonics’’ of Russian Academy of Sciences (RAS).
[6] V.N. Korneev, et al., Nova versi malouglovo˘ i rentgenovsko˘ i apparatury dl issledovani biologiqeskih struktur na stancii diksi v kcsi i nt, Poverhnost~. Rentgenovskie, sinhrotronnye i ne˘ itronnye issledovani vol. 12, 2008, pp. 61–68. [7] H. Tajiri, H. Yamazaki, H. Ohashi, S. Goto, O. Sakata, T. Ishikawa, A middle energy-bandwidth X-ray monochromator for high-flux synchrotron diffraction: revisiting asymmetrically cut silicon crystals, J. Synchrotron Radiat. 26 (3) (2019) 750–755. [8] O. Glatter, O. Kratky, Small Angle X-Ray Scattering, Academic press, 1982. [9] C. Pascual-Izarra, et al., Effortless creation of control & data acquisition graphical user interfaces with Taurus, in: 15th International Conference on Accelerator and Large Experimental Physics Control Systems, ICALEPCS 2015. Conference Proceedings, 2015. [10] A.P. Hammersley, FIT2D: a multi-purpose data reduction, analysis and visualization program, J. Appl. Crystallogr. (2016). [11] A.R. Round, et al., Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33, J. Appl. Crystallogr. (2008). [12] H. Masunaga, K. Sakurai, I. Akiba, K. Ito, M. Takata, Accurate measurements of intrinsic scattering from window materials by use of a vacuum camera, J. Appl. Crystallogr. 46 (2) (2013) 577–579. [13] M.V. Kovalchuk, et al., Investigation of the structure of crystal-forming solutions of potassium dihydrogen phosphate K(H2PO4) (KDP type) on the basis of modeling precursor clusters and according to small-angle X-ray scattering data, Crystallogr. Rep. 64 (1) (2019) 6–10.
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