Structure determination

In order to determine the protein crystal structure the phase problem has to be solved. One commonly used method to solve the phases is the molecular replacement method where an existing protein structure with high sequence (>25%) identity is used as a search model. If there is no homologous protein structure available in the RCSB or PDBe Protein Data Bank the phases can be solved by experimental phasing using heavy atoms such as Pb, Hg, Pt or Au incorporated into the protein crystal by soaking or Se incorporated into the protein by metabolic labeling using Selenomethionine. In the special cases the structure can also be solved by using the anomalous signal from the sulphur atoms present in the protein (Sulphur-SAD).

The crystallographic computing is done in a Linux environment. For structure determination, model building and refinement there are several tools available in the software packages installed on our linux system. The most important software packages are:

For an automated crystal structure determination there is an Auto-Rickshaw web server available at EMBL-Hamburg.

Contact persons:

Ari-Pekka Kvist, PhD, Windows and Linux computing environment
Faculty of Biochemistry and Molecular Medicine F126B
University of Oulu
PO Box 5400, 90014 University of Oulu, Finland
tel. +358-(0)294 481165
e-mail: ari-pekka.kvist (at) oulu.fi

Tiila-Riikka Kiema, PhD
Faculty of Biochemistry and Molecular Medicine F217
University of Oulu
PO Box 5400, 90014 University of Oulu, Finland
tel. +358-(0)294 481179
e-mail: tiila.kiema (at) oulu.fi

Last updated: 12/9/2016