SPIND: A reference-based auto-indexing algorithm for sparse serial crystallography data

Chufeng Li, Xuanxuan Li, Richard Kirian, John Spence, Haiguang Liu, Nadia Zatsepin

    Research output: Contribution to journalArticle

    Abstract

    SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.

    Original languageEnglish (US)
    Pages (from-to)72-84
    Number of pages13
    JournalIUCrJ
    Volume6
    DOIs
    StatePublished - Jan 1 2019

    Fingerprint

    Crystallography
    Diffraction patterns
    crystallography
    Boidae
    Proteins
    Microcrystals
    Rhodopsin
    Opioid Receptors
    Licensure
    Iodine
    Peptides
    Chlorides
    Membrane Proteins
    Ligands
    Membranes
    Crystals
    Molecules
    Acids
    stills
    diffraction patterns

    Keywords

    • Auto-indexing algorithms
    • Bragg peaks
    • Diffract-then-destroy
    • Dynamical studies
    • Electron diffraction
    • Serial crystallography
    • X-ray free-electron lasers
    • XFEL

    ASJC Scopus subject areas

    • Chemistry(all)
    • Biochemistry
    • Materials Science(all)
    • Condensed Matter Physics

    Cite this

    SPIND : A reference-based auto-indexing algorithm for sparse serial crystallography data. / Li, Chufeng; Li, Xuanxuan; Kirian, Richard; Spence, John; Liu, Haiguang; Zatsepin, Nadia.

    In: IUCrJ, Vol. 6, 01.01.2019, p. 72-84.

    Research output: Contribution to journalArticle

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