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Experimental methods for phase determination /MIR,MAD,SAD/ in crystallography of biological macromolecules
Brynda, Jiří
Importance of unbiased phases in post genomic era is emphasized. Article describes the classical methods of phase determination: 1) Multiple Isomorphous replacement, heavy-atom derivative (MIR) 2) Multiple Anomalous Dispersion (MAD) Phasing 3) Single Anomalous Dispersion (SAD) Phasing The better your initial, experimental map is, the more model you will be able to build confidently into this unbiased map before proceeding to phase combination. MAD phases result from perfectly isomorphous data, and do not deteriorate at low resolution as do MIR phases. MIR phases, on the other hand, provide superior phasing power at low resolution resulting in better connectivity. Not surprising, the best maps are either MAD or combined MIR-MAD maps.
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Processing of Diffraction Data Obtained by Oscillation Method on Crystals of Biological Macromolecules
Brynda, Jiří
The components of monochromatic diffractometer suitable for data collection on crystals of biological macromolecules are described, as well as basics of rotation method. The optimal strategy for collecting X-ray diffraction data from macromolecular crystals is discussed. The geometric factors influencing the completeness of data are arising from the symmetry of the reciprocal lattice and from the experimental setup; they affect quantitatively the completeness of the measured set of reflections.
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Validation of macromolecular crystal structures
Řezáčová, Pavlína
X-ray crystallography is the main technique of macromolecular structure determination. Typical problems of protein crystallography diffraction data measured at limited resolution and inaccurate phase informacion adversely affect the quality of electron density maps and consequently the quality of the final model. Currently, there are many methods of protein quality validation. These can be subdivided into two main groups The first group assesses the model quality by evaluating the agreement of the model with the diffraction data. The second group of structure validation methods is based on comparison of the macromolecular model geometrical parameters with standards values derived from the crystal structures of small molecules or high-resolution macromolecular structures. This work is focused on introduction to widely used macromolecular structure-validation software. The main global quality criteria and reliable indicators for detecting local errors are summarized.
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