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

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
–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.