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    ASAP protocol: Crystallization of Enterovirus D68 3C protease (PDB code 8CNX)

    Peter Marples, Lizbé Koekemoer, Daren Fearon, ryan Lithgo

    Published: 2023-12-20 DOI: 10.17504/protocols.io.n92ldm6jnl5b/v1
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    Abstract

    The crystallization protocol and buffer conditions used to obtain Enterovirus D68 3C protease crystals suitable for XChem fragment screening. The crystal structure was depostited to RCSB PDB with code 8CNX.

    Steps

    Equipment needed

    1.

    Formulatrix Rock Imager (or incubator of choice)

    SPT mosquito

    P100 multi-channel pipette

    SwissCI 3 lens plate

    Crystallization experiment

    2.

    Protein and buffer requirements:

    32µL``1millimolar (mM) Sample

    2.88mL

    16µL Sample seeds, dilution 1:100 000

    3.

    Crystallisation screen composition:

    0.1 M Tris-HCl (pH 8.14)

    0.2 M Ammonium acetate

    25% w/v PEG 3350

    Stock solutions used:

    1 M Tris-HCl adjusted to pH 8.14 with HCl

    1 M Ammonium acetate

    50% w/v PEG 3350

    Note
    The crystallisation screen can be stored in a duran bottle or aliquoted into 96 deep well block for easy dispensing into SwissCI 3 lens plates. For long term storage keep the Crystallisation screen in the fridge at 4°C.

    4.

    Prepare seed stock: seed stock:

    1: 100 000 dilution Sample seeds

    5.

    Dispense 30µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.

    Dispense 100nL``1millimolar (mM) Sample to each lens using the SPT mosquito.

    Dispense 200nL to each lens using the SPT mosquito.

    Dispense 50nL to each lens using the SPT mosquito.

    Drop ratio: 1:2:05 ratio (100 nl Sample : 200 nl reservoir solution: 50 nl seeds)

    Final drop volume: 350 nl

    6.

    Incubate at 20°C for 24h 0m 0s in Formulatrix Rock Imager.

    Imaging Schedule : The first images are taken after 12 h and the imaging schedule follows a Fibonacci sequence of days for further collections.

    7.

    Crystal form after ~12 h.

    Citation
    The crystals reach their maximum size after 24 h and most of the precipitant has gone.Crystals typically form either as single crystals or in small clusters containng 4-6 crystals in a flower-like arrangement. Upon mounting a gentle nudge dissociates the cluster.Morphology: typically thin rectangles with pointed ends.Size: ~100 μm in length and ~50 μm in width, depth of the crystals is ~10 μmAppearance : glass shard.Average resolution: 1.5 ÅSpace group: P212121Unit cell: 42.82 Å, 62.53 Å, 147.36 Å 90.00°, 90.00°, 90.00°
    An example of a drop containing EV D68 3C protease crystals.
    An example of a drop containing EV D68 3C protease crystals.

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