6IBQ

Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.

de Wijn, R.Hennig, O.Roche, J.Engilberge, S.Rollet, K.Fernandez-Millan, P.Brillet, K.Betat, H.Morl, M.Roussel, A.Girard, E.Mueller-Dieckmann, C.Fox, G.C.Olieric, V.Gavira, J.A.Lorber, B.Sauter, C.

(2019) IUCrJ 6: 454-464

  • DOI: 10.1107/S2052252519003622
  • Primary Citation of Related Structures:  
    6HW1, 6IBP, 6IBQ, 6Q3T, 6Q52, 6GZP

  • PubMed Abstract: 
  • Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature ...

    Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.


    Related Citations: 
    • A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.
      Masquida, B., Sauter, C., Westhof, E.
      (1999) RNA 5: 1384

    Organizational Affiliation

    Architecture et Réactivité de l'ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA/RNA (5'-R(*CP*GP*UP*GP*AP*UP*CP*G)-D(P*C)-3')A, B9Rattus
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    C [auth B]SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.55 Å
    • R-Value Free: 0.223 
    • R-Value Work: 0.192 
    • R-Value Observed: 0.207 
    • Space Group: H 3
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 40α = 90
    b = 40β = 90
    c = 69.11γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XSCALEdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    French National Research AgencyFranceANR-11-LABX-0057_MITOCROSS
    French National Research AgencyFranceANR-10-LABX-0036_NETRNA
    France--

    Revision History  (Full details and data files)

    • Version 1.0: 2019-05-01
      Type: Initial release
    • Version 1.1: 2019-05-29
      Changes: Data collection, Database references