Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

Classen, Scott; Hura, Greg L.; Holton, James M.; Rambo, Robert P.; Rodic, Ivan; McGuire, Patrick J.; Dyer, Kevin; Hammel, Michal; Meigs, George; Frankel, Kenneth A.; Tainer, John A.

doi:10.1107/s0021889812048698

Title: Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

Journal Article · Thu Jan 17 00:00:00 EST 2013 · Journal of Applied Crystallography

DOI:https://doi.org/10.1107/s0021889812048698· OSTI ID:1625650

Classen, Scott ^[1]; Hura, Greg L. ^[1]; Holton, James M. ^[2]; Rambo, Robert P. ^[1]; Rodic, Ivan ^[3]; McGuire, Patrick J. ^[1]; Dyer, Kevin ^[1]; Hammel, Michal ^[1]; Meigs, George ^[1]; Frankel, Kenneth A. ^[4]; Tainer, John A. ^[3]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Bioscience Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Bioscience Division; Univ. of California, San Francisco, CA (United States). Dept. of Biochemistry and Biophysics
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Engineering Division

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B₄C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625650

Journal Information:: Journal of Applied Crystallography, Vol. 46, Issue 1; ISSN 0021-8898

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing Zhao, W.; Saro, D.; Hammel, M. Nucleic Acids Research, Vol. 42, Issue 2 https://doi.org/10.1093/nar/gkt924	journal	October 2013
HU multimerization shift controls nucleoid compaction Hammel, Michal; Amlanjyoti, Dhar; Reyes, Francis Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1 https://doi.org/10.1107/s0108767317099019	journal	May 2017
Exploring the “minimal” structure of a functional ADAMTS13 by mutagenesis and small-angle X-ray scattering Zhu, Jian; Muia, Joshua; Gupta, Garima Blood, Vol. 133, Issue 17 https://doi.org/10.1182/blood-2018-11-886309	journal	April 2019
Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions Schroer, Martin; Blanchet, Clement E.; Gruzinov, Andrey Yu. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-05671	text	January 2018
Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility Reimer, Janice M.; Eivaskhani, Maximilian; Harb, Ingrid Science, Vol. 366, Issue 6466 https://doi.org/10.1126/science.aaw4388	journal	November 2019
Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions Schroer, Martin A.; Blanchet, Clement E.; Gruzinov, Andrey Yu. Journal of Synchrotron Radiation, Vol. 25, Issue 4 https://doi.org/10.1107/s1600577518007907	journal	June 2018
Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences Hura, Greg L.; Hodge, Curtis D.; Rosenberg, Daniel Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12 https://doi.org/10.1002/prot.25827	journal	August 2019
The role of small-angle scattering in structure-based screening applications Chen, Po-chia; Hennig, Janosch Biophysical Reviews, Vol. 10, Issue 5 https://doi.org/10.1007/s12551-018-0464-x	journal	October 2018
Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers Felberg, Lisa E.; Doshi, Anjali; Hura, Greg L. Figshare https://doi.org/10.6084/m9.figshare.3833526	text	January 2016
Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers Felberg, Lisa E.; Doshi, Anjali; Hura, Greg L. Molecular Physics, Vol. 114, Issue 21 https://doi.org/10.1080/00268976.2016.1224942	journal	September 2016
RNF 4 interacts with both SUMO and nucleosomes to promote the DNA damage response Groocock, Lynda M.; Nie, Minghua; Prudden, John EMBO reports, Vol. 15, Issue 5 https://doi.org/10.1002/embr.201338369	journal	April 2014
Analysis of biostructural changes, dynamics, and interactions – Small-angle X-ray scattering to the rescue Vestergaard, Bente Archives of Biochemistry and Biophysics, Vol. 602 https://doi.org/10.1016/j.abb.2016.02.029	journal	July 2016
Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein Zhang, Senyan; Zhou, Panpan; Wang, Pengfei Cell Reports, Vol. 24, Issue 2 https://doi.org/10.1016/j.celrep.2018.06.041	journal	July 2018
SAXS fingerprints of aldehyde dehydrogenase oligomers Tanner, John J. Data in Brief, Vol. 5 https://doi.org/10.1016/j.dib.2015.10.017	journal	December 2015
Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair Lafrance-Vanasse, Julien; Williams, Gareth J.; Tainer, John A. Progress in Biophysics and Molecular Biology, Vol. 117, Issue 2-3 https://doi.org/10.1016/j.pbiomolbio.2014.12.004	journal	March 2015
FlaF Is a β-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein Banerjee, Ankan; Tsai, Chi-Lin; Chaudhury, Paushali Structure, Vol. 23, Issue 5 https://doi.org/10.1016/j.str.2015.03.001	journal	May 2015
Structural Basis of Substrate Recognition by Aldehyde Dehydrogenase 7A1 Luo, Min; Tanner, John J. Biochemistry, Vol. 54, Issue 35 https://doi.org/10.1021/acs.biochem.5b00754	journal	August 2015
Structural Studies of Yeast Δ ¹ -Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State Pemberton, Travis A.; Srivastava, Dhiraj; Sanyal, Nikhilesh Biochemistry, Vol. 53, Issue 8 https://doi.org/10.1021/bi500048b	journal	February 2014
Evidence That the C-Terminal Domain of a Type B PutA Protein Contributes to Aldehyde Dehydrogenase Activity and Substrate Channeling Luo, Min; Christgen, Shelbi; Sanyal, Nikhilesh Biochemistry, Vol. 53, Issue 35 https://doi.org/10.1021/bi500693a	journal	August 2014
Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding Guo, Hou-Fu; Tsai, Chi-Lin; Terajima, Masahiko Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-02859-z	journal	February 2018
Three-dimensional Imaging of Crystalline Inclusions Embedded in Intact Maize Stalks Badger, John; Lal, Jyotsana; Harder, Ross Scientific Reports, Vol. 3, Issue 1 https://doi.org/10.1038/srep02843	journal	October 2013
Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli Fan, Haitian; Hahm, Joseph; Diggs, Stephen Journal of Biological Chemistry, Vol. 290, Issue 34 https://doi.org/10.1074/jbc.m115.659136	journal	July 2015
Designing and defining dynamic protein cage nanoassemblies in solution Lai, Yen-Ting; Hura, Greg L.; Dyer, Kevin N. Science Advances, Vol. 2, Issue 12 https://doi.org/10.1126/sciadv.1501855	journal	December 2016
Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins Shin, David S.; Pratt, Ashley J.; Tainer, John A. Archaea, Vol. 2014 https://doi.org/10.1155/2014/206735	journal	January 2014
Identifying and Visualizing Macromolecular Flexibility in Structural Biology Palamini, Martina; Canciani, Anselmo; Forneris, Federico Frontiers in Molecular Biosciences, Vol. 3 https://doi.org/10.3389/fmolb.2016.00047	journal	September 2016
Small angle x-ray scattering experiments of monodisperse samples close to the solubility limit Martin, Erik W.; Hopkins, Jesse B.; Mittag, Tanja arXiv https://doi.org/10.48550/arxiv.2003.01278	preprint	January 2020
Wedging open a catalytic site Beuve, Annie eLife, Vol. 8 https://doi.org/10.7554/elife.52418	journal	November 2019

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