1XI1

Phi29 DNA polymerase ssDNA complex, monoclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Correction of X-ray intensities from single crystals containing lattice-translocation defects

Wang, J.Kamtekar, S.Berman, A.J.Steitz, T.A.

(2005) Acta Crystallogr D Biol Crystallogr 61: 67-74

  • DOI: 10.1107/S0907444904026721
  • Primary Citation of Related Structures:  
    1XI1

  • PubMed Abstract: 
  • In 1954, Howells and colleagues described an unusual diffraction pattern from imidazole methemoglobin crystals caused by lattice-translocation defects. In these crystals, two identical lattices coexist as a single coherent mosaic block, but are translated by a fixed vector with respect to each other ...

    In 1954, Howells and colleagues described an unusual diffraction pattern from imidazole methemoglobin crystals caused by lattice-translocation defects. In these crystals, two identical lattices coexist as a single coherent mosaic block, but are translated by a fixed vector with respect to each other. The observed structure is a weighted sum of the two identical but translated structures, one from each lattice; the observed structure factors are a weighted vector sum of the two structure factors with identical unit amplitudes but shifted phases. A general procedure is described to obtain the unit amplitudes of observed structure factors from a realigned single lattice through an X-ray intensity correction. An application of this procedure is made to determine the crystal structure of phi29 DNA polymerase at 2.2 A resolution using multiple isomorphous replacement and multiwavelength anomalous dispersion methods.


    Related Citations: 
    • Correction of X-ray intensities from single crystals containing lattice translocation defects
      Wang, J., Kamtekar, S., Berman, A.J., Steitz, T.A.
      () To be published --: --

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA. wang@mail.csb.yale.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseC [auth A], D [auth B]575Bacillus virus phi29Mutation(s): 2 
Gene Names: 2
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P03680 (Bacillus phage phi29)
Explore P03680 
Go to UniProtKB:  P03680
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(P*TP*TP*TP*TP*T)-3'A [auth C], B [auth D]5N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.277 
    • R-Value Work: 0.243 
    • R-Value Observed: 0.243 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 60.557α = 90
    b = 170.563β = 106.99
    c = 68.813γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling
    MLPHAREphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2004-12-07
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2020-01-22
      Changes: Advisory, Data collection, Derived calculations