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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 (C 10H 16N 2O 3S) 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) (SC-22); USDOE Laboratory Directed Research and Development (LDRD) Program; National Inst. of Health (NIH) (United States)
OSTI Identifier:
1361134
Grant/Contract Number:
AC02-76SF00515; P41GM103393; P41RR001209
Resource Type:
Journal Article: 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.
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. doi: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. 2017. "Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin". United States. doi: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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  • Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox( cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set ofmore » diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less
  • Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data setmore » from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less