5FQ5

Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Data-Collection Strategy for Challenging Native Sad Phasing.

Olieric, V.Weinert, T.Finke, A.D.Anders, C.Li, D.Olieric, N.Borca, C.N.Steinmetz, M.O.Caffrey, M.Jinek, M.Wang, M.

(2016) Acta Crystallogr D Biol Crystallogr 72: 421

  • DOI: 10.1107/S2059798315024110
  • Primary Citation of Related Structures:  
    5DWK, 5FQ5

  • PubMed Abstract: 
  • Recent improvements in data-collection strategies have pushed the limits of native SAD (single-wavelength anomalous diffraction) phasing, a method that uses the weak anomalous signal of light elements naturally present in macromolecules. These involve the merging of multiple data sets from either multiple crystals or from a single crystal collected in multiple orientations at a low X-ray dose ...

    Recent improvements in data-collection strategies have pushed the limits of native SAD (single-wavelength anomalous diffraction) phasing, a method that uses the weak anomalous signal of light elements naturally present in macromolecules. These involve the merging of multiple data sets from either multiple crystals or from a single crystal collected in multiple orientations at a low X-ray dose. Both approaches yield data of high multiplicity while minimizing radiation damage and systematic error, thus ensuring accurate measurements of the anomalous differences. Here, the combined use of these two strategies is described to solve cases of native SAD phasing that were particular challenges: the integral membrane diacylglycerol kinase (DgkA) with a low Bijvoet ratio of 1% and the large 200 kDa complex of the CRISPR-associated endonuclease (Cas9) bound to guide RNA and target DNA crystallized in the low-symmetry space group C2. The optimal native SAD data-collection strategy based on systematic measurements performed on the 266 kDa multiprotein/multiligand tubulin complex is discussed.


    Organizational Affiliation

    Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1B1372Streptococcus pyogenesMutation(s): 2 
Gene Names: cas9csn1SPy_1046
EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Explore Q99ZW2 
Go to UniProtKB:  Q99ZW2
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SGRNAA84synthetic construct
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    TARGET DNA STRAND PROXIMAL FRAGMENTC11synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      NON-TARGET DNA STRANDD11synthetic construct
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        TARGET DNA STRAND DISTAL FRAGMENTE17synthetic construct
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 2 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        K
        Query on K

        Download Ideal Coordinates CCD File 
        H [auth A] , I [auth A] , J [auth A] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , 
        H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth D]
        POTASSIUM ION
        K
        NPYPAHLBTDXSSS-UHFFFAOYSA-N
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        F [auth A], G [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.14 Å
        • R-Value Free: 0.225 
        • R-Value Work: 0.191 
        • R-Value Observed: 0.192 
        • Space Group: C 1 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 177.74α = 90
        b = 67.57β = 111.31
        c = 188.19γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        XDSdata reduction
        XSCALEdata scaling
        SHELXphasing

        Structure Validation

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        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2016-03-23
          Type: Initial release
        • Version 2.0: 2019-10-23
          Changes: Atomic model, Data collection, Other