8SIL

Lysozyme crystallized in cyclic olefin copolymer-based microfluidic chips


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.

Liu, Z.Gu, K.K.Shelby, M.L.Gilbile, D.Lyubimov, A.Y.Russi, S.Cohen, A.E.Narayanasamy, S.R.Botha, S.Kupitz, C.Sierra, R.G.Poitevin, F.Gilardi, A.Lisova, S.Coleman, M.A.Frank, M.Kuhl, T.L.

(2023) Acta Crystallogr D Struct Biol 79: 944-952

  • DOI: https://doi.org/10.1107/S2059798323007027
  • Primary Citation of Related Structures:  
    8FZW, 8SCY, 8SIL

  • PubMed Abstract: 

    Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.


  • Organizational Affiliation

    Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.8α = 90
b = 78.8β = 90
c = 38γ = 90
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
CrystFELdata collection
XDSdata reduction
pointlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary