The Link to X-Ray Protein Crystallography


A. Crystal Production

(wet lab)

  1. Production
  2. Purification
  3. Crystallisation

 

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B. Data Collection

(x-ray lab)

  1. Mounting
  2. Shooting
  3. Detection

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C. Structure Solution

(computer lab)

  1. Indexing
  2. Integration
  3. Scaling
  4. Phasing
  5. Building
  6. Refinement
  7. Validation
  8. Publication

Direct methods

For small molecules there are methods to "guess" the phases of the structure factors. One possiblity is the Patterson map. This is a map produced by setting all phases to zero. The amplitudes of each refelction still result in a map that contains information. This information can be interpreted as vectors between atoms, which allows to think of a molecule that explains the map. Using this method molecules up to 100 atoms can be solved by hand and up to 1000 atoms can be solved by progammes. This is not enough for proteins but enough to solve the heavy atom substructures for isomorphous replacement and anomalous dispersion, which in turn allows to solve the phases of the protein diffraction data. There are also other direct methods.

A Patterson map can be constructed by taking all vectors between atoms from the molecule (top) and plotting them from the origins of the unit cell (bottom). The peaks at the origins contain all the vectors between the atoms themselves and thus have a hight corresponding to the number of atoms in the molecule.

LINKS

Structure Factor Tutorial (Cowtan)

OTHER METHODS:

Molecular replacement (MR)
Isomorphous replacement (SIR, MIR)
Anomalous dispersion (SAD, MAD)
Combination of methods (SIRAS, MIRAS)


Mission / Organisations / Trivia / Links / Florian Fisch / 5 June 2009