Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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
+ Show Author Affiliations
  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. doi:10.1038/sdata.2017.55.
Copy to clipboard
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
Copy to clipboard
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.
Copy to clipboard
@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}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/sdata.2017.55
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

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

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

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

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

Characterization and use of the spent beam for serial operation of LCLS
journal, April 2015

  • Boutet, Sébastien; Foucar, Lutz; Barends, Thomas R. M.
  • Journal of Synchrotron Radiation, Vol. 22, Issue 3
  • DOI: 10.1107/S1600577515004002

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

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

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

X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92
journal, July 1993

  • 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

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

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

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

Coherent Soft X-ray Diffraction Imaging of Coliphage PR772 at the Linac Coherent Light Source
dataset, January 2016

  • Reddy, H.
  • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Uppsala University, CFEL, Arizona State University, La Trobe University, University of Wisconsin, SLAC National Accelerator Laboratory
  • DOI: 10.11577/1343368

Coherent Soft X-ray Diffraction Imaging of Coliphage PR772 at the Linac Coherent Light Source
dataset, January 2016

  • Reddy, H.
  • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Uppsala University, CFEL, Arizona State University, La Trobe University, University of Wisconsin, SLAC National Accelerator Laboratory
  • DOI: 10.11577/1343369

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021

Coherent Soft X-ray Diffraction Imaging of Coliphage PR772 at the Linac Coherent Light Source
dataset, January 2017

  • Reddy, Hemanth
  • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Uppsala University, SLAC National Accelerator Laboratory, CFEL, University of Hamburg, Arizona State University, University of Wisconsin, La Trobe University
  • DOI: 10.11577/1349664

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

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Use cases of lossy compression for floating-point data in scientific data sets
    journal, May 2019

    • Cappello, Franck; Di, Sheng; Li, Sihuan
    • The International Journal of High Performance Computing Applications, Vol. 33, Issue 6
    • DOI: 10.1177/1094342019853336

    Climbing the Data Mountain: Processing of SFX Data
    text, January 2018

      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: