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  • International Union of Crystallography (IUCr)  (22)
  • 1
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2017
    In:  Journal of Synchrotron Radiation Vol. 24, No. 1 ( 2017-01-01), p. 29-41
    In: Journal of Synchrotron Radiation, International Union of Crystallography (IUCr), Vol. 24, No. 1 ( 2017-01-01), p. 29-41
    Abstract: Serial crystallography, in which single-shot diffraction images are collected, has great potential for protein microcrystallography. Although serial femtosecond crystallography (SFX) has been successfully demonstrated, limited beam time prevents its routine use. Inspired by SFX, serial synchrotron crystallography (SSX) has been investigated at synchrotron macromolecular crystallography beamlines. Unlike SFX, the longer exposure time of milliseconds to seconds commonly used in SSX causes radiation damage. However, in SSX, crystals can be rotated during the exposure, which can achieve efficient coverage of the reciprocal space. In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25° was the best rotation step for the achievable resolution limit, whereas a rotation step larger than or equal to 1° was favorable for Hg-SAD phasing. Although an accumulated dose beyond 1.1 MGy caused specific damage at the Hg site, increases in resolution and anomalous signal were observed up to 3.4 MGy because of a higher signal-to-noise ratio.
    Type of Medium: Online Resource
    ISSN: 1600-5775
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2017
    detail.hit.zdb_id: 2021413-3
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  • 2
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2014
    In:  Acta Crystallographica Section A Foundations and Advances Vol. 70, No. a1 ( 2014-08-05), p. C331-C331
    In: Acta Crystallographica Section A Foundations and Advances, International Union of Crystallography (IUCr), Vol. 70, No. a1 ( 2014-08-05), p. C331-C331
    Abstract: BL41XU is the oldest macromolecular crystallography (MX) beamline at SPring-8 [1]. Although it has been contributing to the structure determination of difficult samples since its start of operation in 1997, the targets for the structural study is still getting more challenging and the crystal quality brought to the beamline is getting worse. Therefore, we have upgraded the focusing optics and diffractometer of BL41XU to cope with these targets. Our goal is to achieve an environment which can offer a stable beam with a photon flux of 〉 10 1 3 photons/s in the beam size range of 5 ~ 50μm. It is a complementary specification with our micro-focus beamline BL32XU [2], and allows both micro-crystallography and data collection using crystal volume. The new optics adopts a two-step focusing with elliptical figured mirrors: the first optics is a single horizontal mirror and the second one adopts Kirkpatrick–Baez (KB) configuration. At the middle of the two focusing optics, a high precision horizontal slit is installed to define secondary source size. The beam size can be changed either by changing the secondary source size, by offsetting the sample position, or by tilting the vertical mirror. For the stable use of small beam, both KB mirror and diffractometer were equipped on the granite stage, and enclosed in a booth in which the temperature is keep stable. On the new diffractometer, we equipped PILATUS3 6M that enables rapid data collection combining with high flux beam. Together with the upgrade of hardware, software tools, which support diffraction based centering and determination of measurement condition, have been implemented in order to make full use of the renewed beamline. The upgrade was conducted in the long shut-down period between January and March of this year, and the beamline was opened for users in the middle of May after commissioning of one month. The result of commissioning and initial results will be presented. This study was supported by the MEXT of Japan.
    Type of Medium: Online Resource
    ISSN: 2053-2733
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2014
    detail.hit.zdb_id: 2020844-3
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  • 3
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2016
    In:  Acta Crystallographica Section A Foundations and Advances Vol. 72, No. a1 ( 2016-08-28), p. s21-s21
    In: Acta Crystallographica Section A Foundations and Advances, International Union of Crystallography (IUCr), Vol. 72, No. a1 ( 2016-08-28), p. s21-s21
    Type of Medium: Online Resource
    ISSN: 2053-2733
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2016
    detail.hit.zdb_id: 2020844-3
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  • 4
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2014
    In:  Acta Crystallographica Section A Foundations and Advances Vol. 70, No. a1 ( 2014-08-05), p. C352-C352
    In: Acta Crystallographica Section A Foundations and Advances, International Union of Crystallography (IUCr), Vol. 70, No. a1 ( 2014-08-05), p. C352-C352
    Abstract: On BL32XU, a microfocus beamline at SPring-8, oscillation data are collected with typical horizontal beam size of 1 μm. Hence it requires very accurate crystal centering, which is difficult especially for invisible crystals e.g. LCP crystals. Therefore, we perform raster diffraction scan to find crystal positions based on their diffractivity using low-dose exposure. It had been time consuming process due to two reasons; i) slow readout time of CCD, ii) manual inspection of hundreds of diffraction images. To tackle this problem, we installed new fast-readout CCD detector, MX225HS (Rayonix, L.L.C.), and developed support tool for raster scan based crystal centering. The tool visually shows possible crystal position on 2D map based on spot populations, and therefore it is named SHIKA (Spot-wo Hirotte Ichiwo Kimeru Application; a Japanese abbreviation which means the application for crystal positioning by picking up spots). SHIKA automatically detects new images when raster scan started and finishes just after raster scan ends. On GUI, user can find and pass the crystal position information to KUMA (a tool suggesting helical data collection strategy with predicted radiation damage) to start data collection immediately. User can also see picked spots on diffraction images with GUI. SHIKA has been developed based on DISTL [1] and modified to be faster and more accurate, especially for LCP crystal which is an important target on BL32XU. SHIKA picks up spots after subtracting smoothed pseudo-background which is a key for better separation of spots and ring-like diffuse background of lipids. Smoothing is time-consuming, but SHIKA now uses GPUs for almost all process including high-speed median filter [2] so that it can be done within ~100 msec. Further development is under way for faster processing. Now SHIKA can be also used on BL41XU, a high flux beamline at SPring-8 with some adjustment for PILATUS3 (Detectris Ltd.) detector.
    Type of Medium: Online Resource
    ISSN: 2053-2733
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2014
    detail.hit.zdb_id: 2020844-3
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  • 5
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2017
    In:  Acta Crystallographica Section A Foundations and Advances Vol. 73, No. a2 ( 2017-12-01), p. C1027-C1027
    In: Acta Crystallographica Section A Foundations and Advances, International Union of Crystallography (IUCr), Vol. 73, No. a2 ( 2017-12-01), p. C1027-C1027
    Type of Medium: Online Resource
    ISSN: 2053-2733
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2017
    detail.hit.zdb_id: 2020844-3
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  • 6
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2018
    In:  Acta Crystallographica Section A Foundations and Advances Vol. 74, No. a1 ( 2018-07-20), p. a337-a337
    In: Acta Crystallographica Section A Foundations and Advances, International Union of Crystallography (IUCr), Vol. 74, No. a1 ( 2018-07-20), p. a337-a337
    Type of Medium: Online Resource
    ISSN: 2053-2733
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2018
    detail.hit.zdb_id: 2020844-3
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  • 7
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2020
    In:  Acta Crystallographica Section D Structural Biology Vol. 76, No. 2 ( 2020-02-01), p. 155-165
    In: Acta Crystallographica Section D Structural Biology, International Union of Crystallography (IUCr), Vol. 76, No. 2 ( 2020-02-01), p. 155-165
    Abstract: Reducing the sample-exchange time is a crucial issue in maximizing the throughput of macromolecular crystallography (MX) beamlines because the diffraction data collection itself is completed within a minute in the era of pixel-array detectors. To this end, an upgraded sample changer, SPACE-II, has been developed on the basis of the previous model, SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), at the BL41XU beamline at SPring-8. SPACE-II achieves one sample-exchange step within 16 s, of which its action accounts for only 11 s, because of three features: (i) the implementation of twin arms that enable samples to be exchanged in one cycle of mount-arm action, (ii) the implementation of long-stroke mount arms that allow samples to be exchanged without withdrawal of the detector and (iii) the use of a fast-moving translation and rotation stage for the mount arms. By pre-holding the next sample prior to the sample-exchange sequence, the time was further decreased to 11 s in the case of automatic data collection, of which the action of SPACE-II accounted for 8 s. Moreover, the sample capacity was expanded from four to eight Uni-Pucks. The performance of SPACE-II has been demonstrated in over two years of operation at BL41XU; the average number of samples mounted on the diffractometer in one day was increased from 132 to 185, with an error rate of 0.089%, which counted incidents in which users could not continue with an experiment without recovery work by entering the experimental hutch. On the basis of these results, SPACE-II has been installed at three other MX beamlines at SPring-8 as of July 2019. The fast and highly reliable SPACE-II is now one of the most important pieces of infrastructure for the MX beamlines at SPring-8, providing users with the opportunity to fully make use of limited beamtime with brilliant X-rays.
    Type of Medium: Online Resource
    ISSN: 2059-7983
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2020
    detail.hit.zdb_id: 2968623-4
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  • 8
    In: Journal of Synchrotron Radiation, International Union of Crystallography (IUCr), Vol. 11, No. 4 ( 2004-07-01), p. 343-346
    Type of Medium: Online Resource
    ISSN: 0909-0495
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2004
    detail.hit.zdb_id: 2021413-3
    SSG: 13
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  • 9
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2014
    In:  Acta Crystallographica Section A Foundations and Advances Vol. 70, No. a1 ( 2014-08-05), p. C333-C333
    In: Acta Crystallographica Section A Foundations and Advances, International Union of Crystallography (IUCr), Vol. 70, No. a1 ( 2014-08-05), p. C333-C333
    Abstract: Protein micro-crystallography is one of the most advanced technologies for protein structure analysis. In order to realize this, an undulator beamline, named BL32XU, was constructed at SPring-8. The beamline can provide beam with size of 0.9 x 0.9 µm and photon flux of 6E10 photons/s. The beam size can be easily changed by users from 1 to 10 µm square with the same flux density. Through three years user operation, we have established several key systems for efficient protein micro-crystallography. One of them is the software for precise positioning of micro-crystals in `raster scan'. SHIKA is a program with GUI which searches diffraction spots in a plenty of low dose diffraction images obtained in raster scan. Finally, it generates 2D map of crystal positions based on the number of spots or spot intensities. Parameters and thresholds in peak search have been empirically optimized for LCP crystals and it provides robust results. Another system is for the data collection strategy. Almost all successful data collections were conducted via `helical data collection' on BL32XU using the line-focused beam. The GUI software, named KUMA, enables estimation of an accumulated dose and suggests suitable experimental conditions for helical data collection. The system is proven to be useful for experimental phasing using tiny LCP crystals of membrane proteins[1-3]. Based on them, the rapid and automatic data collection system using protein micro-crystals is under development. The new CCD detector, Rayonix MX225HS, was installed for faster data acquisition in 10 Hz with the pixel size of 78 µm square. The new SHIKA using GPUs is under development for faster and more accurate crystal alignment. Following this step, KUMA system can suggest experimental conditions for each crystal found on the loop. We also report about the effects of higher dose rate in protein crystallography up to the order of 100 MGy/s. This work was supported by Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology, Japan.
    Type of Medium: Online Resource
    ISSN: 2053-2733
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2014
    detail.hit.zdb_id: 2020844-3
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  • 10
    Online Resource
    Online Resource
    International Union of Crystallography (IUCr) ; 2020
    In:  Acta Crystallographica Section F Structural Biology Communications Vol. 76, No. 12 ( 2020-12-01), p. 616-622
    In: Acta Crystallographica Section F Structural Biology Communications, International Union of Crystallography (IUCr), Vol. 76, No. 12 ( 2020-12-01), p. 616-622
    Abstract: Cryocrystallography is a technique that is used more often than room-temperature data collection in macromolecular crystallography. One of its advantages is the significant reduction in radiation damage, which is especially useful in synchrotron experiments. Another advantage is that cryopreservation provides simple storage of crystals and easy transportation to a synchrotron. However, this technique sometimes results in the undesirable adhesion of frost to mounted crystals. The frost produces noisy diffraction images and reduces the optical visibility of crystals, which is crucial for aligning the crystal position with the incident X-ray position. To resolve these issues, a computer-controlled device has been developed that drizzles liquid nitrogen over a crystal to remove frost. It was confirmed that the device works properly, reduces noise from ice rings in diffraction images and enables the centering of crystals with low visibility owing to frost adhesion.
    Type of Medium: Online Resource
    ISSN: 2053-230X
    Language: Unknown
    Publisher: International Union of Crystallography (IUCr)
    Publication Date: 2020
    detail.hit.zdb_id: 2175956-X
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