Data Analysis WorkbeNch (DAWN) Basham, Mark; Filik, Jacob; Wharmby, Michael T. ...
Journal of synchrotron radiation,
20/May , Volume:
22, Issue:
3
Journal Article
Peer reviewed
Open access
Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed ...to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single‐crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientific area.
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A departure from a linear or an exponential intensity decay in the diffracting power of protein crystals as a function of absorbed dose is reported. The observation of a lag phase raises the ...possibility of collecting significantly more data from crystals held at room temperature before an intolerable intensity decay is reached. A simple model accounting for the form of the intensity decay is reintroduced and is applied for the first time to high frame‐rate room‐temperature data collection.
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A correction in the paper by Lazo et al. (2021). J. Synchrotron Rad.28, 1649–1661 is made.
A correction in the paper by Lazo et al. (2021). J. Synchrotron Rad.28, 1649–1661 is made.
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A novel raster‐scanning method combining continuous sample translation with the fast readout of a Pilatus P6M detector has been developed on microfocus beamline I24 at Diamond Light Source. This fast ...grid‐scan tool allows the rapid evaluation of large sample volumes without the need to increase the beam size at the sample through changes in beamline hardware. A slow version is available for slow‐readout detectors. Examples of grid‐scan use in centring optically invisible samples and in detecting and characterizing numerous microcrystals on a mesh‐like holder illustrate the most common applications of the grid scan now in routine use on I24.
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The highly automated macromolecular crystallography beamline AMX/17‐ID‐1 is an undulator‐based high‐intensity (>5 × 1012 photons s−1), micro‐focus (7 µm × 5 µm), low‐divergence (1 mrad × 0.35 mrad) ...energy‐tunable (5–18 keV) beamline at the NSLS‐II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17‐ID with the FMX beamline, the frontier micro‐focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro‐focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17‐ID‐1 as well as some plans for the near future are presented.
AMX (17‐ID‐1) is the highly automated macromolecular crystallography beamline at the NSLS‐II. Photon delivery system, beamline instrumentation, high‐performance computing environment and suites of applications are described for beamline scientists and users. AMX's primary mission is to support routine structure determination from the most challenging projects.
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Exceptionally large crystals of posnjakite, Cu
SO
(OH)
(H
O), formed during corrosion of a Swagelock(tm) Snubber copper gasket within the MX1 beamline at the ANSTO-Melbourne, Australian Synchrotron. ...The crystal structure was solved using synchrotron radiation to
= 0.029 and revealed a structure based upon Cu
(OH)
(H
O)O sheets, which contain Jahn-Teller-distorted Cu octa-hedra. The sulfate tetra-hedra are bonded to one side of the sheet
corner sharing and linked to successive sheets
extensive hydrogen bonds. The sulfate tetra-hedra are split and rotated, which enables additional hydrogen bonds.
MX2 is an in‐vacuum undulator‐based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X‐rays in the energy range 4.8–21 keV to a focal spot of 22 × 12 µm FWHM ...(H × V). At 13 keV the flux at the sample is 3.4 × 1012 photons s−1. The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard‐to‐crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. The beamline is now mature and has enjoyed a full user program for the last nine years. This paper describes the beamline status, plans for its future and some recent scientific highlights.
A microfocus macromolecular crystallography beamline at the Australian Synchrotron is presented.
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Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 Schneider et al. (2013). J. Phys. ...Conf. Ser.425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser.493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006. FMX, the micro‐focusing Frontier MX beamline in sector 17‐ID‐2 at NSLS‐II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s−1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s−1 at final storage‐ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre‐sized crystals, raster optimization of diffraction from inhomogeneous crystals, high‐resolution data collection from large‐unit‐cell crystals, room‐temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample‐screening and ligand‐binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample‐delivery methods have been implemented, such as an ultra‐high‐speed high‐precision piezo scanner goniometer Gao et al. (2018). J. Synchrotron Rad.25, 1362–1370, new microcrystal‐optimized micromesh well sample holders Guo et al. (2018). IUCrJ, 5, 238–246 and highly viscous media injectors Weierstall et al. (2014). Nat. Commun.5, 3309. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult‐to‐crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.
The new Frontier Microfocus Macromolecular Crystallography beamline FMX in sector 17‐ID‐2 of the National Synchrotron Lightsource II provides an ultra‐bright microfocus beam and a flexible experimental station for structure determination from the most challenging crystals.
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