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Crystallographic Databases

Crystallographic Databases. I590 Spring 2005 Based in part on slides from John C. Huffman. Crystallography Databases. Significance: Complete crystallographic analysis leads to 3-dimensional structural data. Crystallography Databases. Coordinate Systems Crystallographic coordinates

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Crystallographic Databases

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  1. Crystallographic Databases I590 Spring 2005 Based in part on slides from John C. Huffman

  2. Crystallography Databases Significance: Complete crystallographic analysis leads to 3-dimensional structural data.

  3. Crystallography Databases Coordinate Systems Crystallographic coordinates Cartesian coordinates

  4. Crystallographic Coordinates • Almost all crystallographic results are reported in this manner, with a range of 0 to 1. • In the center of the unit cell, the measurement would be ½, ½, ½

  5. Crystallographic Coordinates

  6. Cartesian Coordinates Cartesian coordinates are reported in Angstroms, usually with the first atom at 0,0,0; second atom at x,0,0, and third atom at x,y,0. Of the major crystallographic databases, only PDB uses Cartesian coordinates.

  7. Concept of the Unit Cell • Depicts the repeating unit in a crystal structure • Has 3 sides and 3 angles • Lengths are designated a, b, c • Angles are designated α, β, γ • α lies between the b and c axes

  8. Symmetry and Space Groups • Crystal lattices formed from 17 plane groups, 32 point groups, 230 space groups • A point group is the complete collection of all symmetry elements passing through a central point, describing the symmetry of an individual object. • A space group is the complete collection of all symmetry elements of an infinitely repeating pattern.

  9. Crystallography Databases Available Databases PDB: Protein Data Bank ICSD: Inorganic Crystal Structure Database CSD: Cambridge Structural Database CRYSTMET: Metals Database

  10. PDB: Protein Data Bank http://www.rcsb.org/pdb/ Contained 16,433 Structures on October 31, 2001 Contained 30,453 structures on April 12, 2005

  11. ICSD: Inorganic Crystal Structure Database • includes pure elements, minerals, metals, and intermetallic compounds (with atomic coordinates published since 1913) • contained 82,676 entries as of November 2004 • updated twice a year, with each update having about 2000 new records • Windows PC, Linux, & Web versions

  12. ICSD

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  23. CSD: Cambridge Structural Database • Small molecule crystal structures • http://www.ccdc.cam.ac.uk/products/csd/ • Organic molecules (including peptides up to 24 residues) • Metal-organic compounds • 335,276 entries as of January 1, 2005 • 303,733 different compounds • Single crystal or Powder Diffraction studies • Determined by X-Ray or Neutron Diffraction

  24. CSD Components • Search and information retrieval (ConQuest) • Structure visualization (Mercury) • Manipulation of results and numerical analysis (Vista) • Database creation (PreQuest)

  25. Other CCDC Products • Libraries of extracted molecular and intermolecular geometry information organized according to molecular fragments and functional groups • Mogul contains bond lengths, valence, and torsion angles and displays results as histograms and associated statistical data • IsoStar is a knowledge base of intermolecular interactions, containing data derived from both the CSD and the PDB, with data displayed as scatterplots or contoured maps

  26. CCDC’s GOLD • Uses a genetic algorithm to dock flexible lligands in to partially flexible protein binding sites • Uses torsion angle distributions from the CSD to restrict ligand conformations

  27. CCDC’s Superstar • Uses information on intermolecular interactions found in IsoStar to identify regions within protein cavities or around molecules where selected functional groups are likely to interact favorably.

  28. CCDC’s Relibase+ • Features detailed analysis of superimposed ligand and binding sites, ligand similarity, and substructure searches • Based on structures in the PDB and a proprietary collection that the user may have • Enables investigation of crystallographic packing effects around ligand binding sites • Includes info about bound water molecules

  29. CIF: Crystallographic Information Format • standard means of information interchange in crystallography, sponsored by the International Union of Crystallography (IUCr) • CCDC program enCIFer provides an intuitive, user-friendly interface to facilitate the editing and validation of CIFs • Nearly all info submitted to the CCDC is in CIF format now

  30. Powder Diffraction File • http://www.icdd.com/products/overview.htm • PDF for 2004 had 355,303 entries • Versions: • For Inorganic • Organic/organometallic • Used for materials for which it is difficult to obtain a single crystal (e.g., metals)

  31. Crystal Structure Viewers • PDB formats can be viewed with a variety of viewers. • CIF format viewers are being developed. • RasMol is one of the best viewers readily available at no charge.

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