Crystallographic Databases

I590Spring 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–Cartesian coordinates

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

Crystallographic Coordinates

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.

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

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.

Crystallography Databases

• Available Databases–PDB: Protein Data Bank–ICSD: Inorganic Crystal Structure Database–CSD: Cambridge Structural Database–CRYSTMET: Metals Database

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

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

ICSD

ICSD

ICSD

ICSD

ICSD

ICSD

ICSD

ICSD

ICSD

ICSD

ICSD

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

CSD Components

• Search and information retrieval (ConQuest)

• Structure visualization (Mercury)

• Manipulation of results and numerical analysis (Vista)

• Database creation (PreQuest)

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

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

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.

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

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

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)

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.