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Title: Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin

Abstract

We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C10H16N2O3S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously. Diffraction patterns from Se-B SA were recorded to a resolution of 1.9 Å. The dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) and also on LCLS compute nodes as a resource for research and algorithm development.

Authors:
 [1]; ORCiD logo [2];  [1];  [3];  [1];  [4];  [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [5];  [1];  [6];  [1];  [1];  [1];  [1];  [1] more »;  [1];  [5];  [1];  [7];  [1] « less
  1. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source
  2. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford PULSE Inst. Biosciences Division. Stanford Synchrotron Radiation Lightsource
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford PULSE Inst. Biosciences Division
  4. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford PULSE Inst.
  5. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source. Biosciences Division
  6. SLAC National Accelerator Lab., Menlo Park, CA (United States). Biosciences Division
  7. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource; Univ. of California, San Francisco, CA (United States). Dept. of Biochemistry and Biophysics
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Laboratory Directed Research and Development (LDRD) Program; National Inst. of Health (NIH) (United States)
Contributing Org.:
Univ. of California, San Francisco, CA (United States)
OSTI Identifier:
1361134
Grant/Contract Number:  
AC02-76SF00515; P41GM103393; P41RR001209
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; 36 MATERIALS SCIENCE; Nanocrystallography; Macromolecules and clusters; Imaging; Biological physics

Citation Formats

Yoon, Chun Hong, DeMirci, Hasan, Sierra, Raymond G., Dao, E. Han, Ahmadi, Radman, Aksit, Fulya, Aquila, Andrew L., Batyuk, Alexander, Ciftci, Halilibrahim, Guillet, Serge, Hayes, Matt J., Hayes, Brandon, Lane, Thomas J., Liang, Meng, Lundström, Ulf, Koglin, Jason E., Mgbam, Paul, Rao, Yashas, Rendahl, Theodore, Rodriguez, Evan, Zhang, Lindsey, Wakatsuki, Soichi, Boutet, Sébastien, Holton, James M., and Hunter, Mark S. Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin. United States: N. p., 2017. Web. https://doi.org/10.1038/sdata.2017.55.
Yoon, Chun Hong, DeMirci, Hasan, Sierra, Raymond G., Dao, E. Han, Ahmadi, Radman, Aksit, Fulya, Aquila, Andrew L., Batyuk, Alexander, Ciftci, Halilibrahim, Guillet, Serge, Hayes, Matt J., Hayes, Brandon, Lane, Thomas J., Liang, Meng, Lundström, Ulf, Koglin, Jason E., Mgbam, Paul, Rao, Yashas, Rendahl, Theodore, Rodriguez, Evan, Zhang, Lindsey, Wakatsuki, Soichi, Boutet, Sébastien, Holton, James M., & Hunter, Mark S. Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin. United States. https://doi.org/10.1038/sdata.2017.55
Yoon, Chun Hong, DeMirci, Hasan, Sierra, Raymond G., Dao, E. Han, Ahmadi, Radman, Aksit, Fulya, Aquila, Andrew L., Batyuk, Alexander, Ciftci, Halilibrahim, Guillet, Serge, Hayes, Matt J., Hayes, Brandon, Lane, Thomas J., Liang, Meng, Lundström, Ulf, Koglin, Jason E., Mgbam, Paul, Rao, Yashas, Rendahl, Theodore, Rodriguez, Evan, Zhang, Lindsey, Wakatsuki, Soichi, Boutet, Sébastien, Holton, James M., and Hunter, Mark S. Tue . "Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin". United States. https://doi.org/10.1038/sdata.2017.55. https://www.osti.gov/servlets/purl/1361134.
@article{osti_1361134,
title = {Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin},
author = {Yoon, Chun Hong and DeMirci, Hasan and Sierra, Raymond G. and Dao, E. Han and Ahmadi, Radman and Aksit, Fulya and Aquila, Andrew L. and Batyuk, Alexander and Ciftci, Halilibrahim and Guillet, Serge and Hayes, Matt J. and Hayes, Brandon and Lane, Thomas J. and Liang, Meng and Lundström, Ulf and Koglin, Jason E. and Mgbam, Paul and Rao, Yashas and Rendahl, Theodore and Rodriguez, Evan and Zhang, Lindsey and Wakatsuki, Soichi and Boutet, Sébastien and Holton, James M. and Hunter, Mark S.},
abstractNote = {We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C10H16N2O3S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously. Diffraction patterns from Se-B SA were recorded to a resolution of 1.9 Å. The dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) and also on LCLS compute nodes as a resource for research and algorithm development.},
doi = {10.1038/sdata.2017.55},
journal = {Scientific Data},
number = ,
volume = 4,
place = {United States},
year = {2017},
month = {4}
}

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    Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser
    journal, November 2016

    • Hunter, Mark S.; Yoon, Chun Hong; DeMirci, Hasan
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms13388

    CrystFEL : a software suite for snapshot serial crystallography
    journal, March 2012

    • White, Thomas A.; Kirian, Richard A.; Martin, Andrew V.
    • Journal of Applied Crystallography, Vol. 45, Issue 2
    • DOI: 10.1107/s0021889812002312

    Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II
    journal, November 2015

    • Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan
    • Nature Methods, Vol. 13, Issue 1
    • DOI: 10.1038/nmeth.3667

    Linac Coherent Light Source data analysis using psana
    journal, March 2016

    • Damiani, D.; Dubrovin, M.; Gaponenko, I.
    • Journal of Applied Crystallography, Vol. 49, Issue 2
    • DOI: 10.1107/s1600576716004349

    Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation.
    journal, April 1989

    • Hendrickson, W. A.; Pahler, A.; Smith, J. L.
    • Proceedings of the National Academy of Sciences, Vol. 86, Issue 7
    • DOI: 10.1073/pnas.86.7.2190

    Recent developments in CrystFEL
    journal, March 2016

    • White, Thomas A.; Mariani, Valerio; Brehm, Wolfgang
    • Journal of Applied Crystallography, Vol. 49, Issue 2
    • DOI: 10.1107/s1600576716004751

    PHENIX: a comprehensive Python-based system for macromolecular structure solution
    journal, January 2010

    • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
    • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
    • DOI: 10.1107/s0907444909052925

    The Coherent X-ray Imaging instrument at the Linac Coherent Light Source
    journal, April 2015

    • Liang, Mengning; Williams, Garth J.; Messerschmidt, Marc
    • Journal of Synchrotron Radiation, Vol. 22, Issue 3
    • DOI: 10.1107/s160057751500449x

    X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92
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    • Henke, B. L.; Gullikson, E. M.; Davis, J. C.
    • Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342
    • DOI: 10.1006/adnd.1993.1013

    Experience with the CSPAD during dedicated detector runs at LCLS
    journal, March 2014


    First lasing and operation of an ångstrom-wavelength free-electron laser
    journal, August 2010


    Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
    journal, May 2014

    • Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C.
    • Journal of Applied Crystallography, Vol. 47, Issue 3
    • DOI: 10.1107/s1600576714007626

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