Introduction to Bionanotechnology by Young-Chul Lee & Ju-Young Moon

Author:Young-Chul Lee & Ju-Young Moon
Language: eng
Format: epub
ISBN: 9789811512933
Publisher: Springer Singapore

As mentioned above, the electron density map, which allows us to observe the density of electrons in the structure of the crystal, is the result obtained when using X-ray crystallography analysis. A very influential factor to this map is the quality of the analytical samples, more specifically, the quality of the analytical crystals. It will affect the resolution of the map or the distance between the electron density points on the map. Therefore, high crystal quality will result in excellent resolution. Then the components of the crystal - or molecule - with a distance less than 1 Angstrom unit Å, will also be analyzed and displayed in a more straightforward and more precise way. For example, with low resolution 3.0Å, we will need more analysis and covalent to explain and determine the distance between points when they are less resolution. In resolution 1.5Å, single atoms are displayed more easily [6]. Once we have a map with a high resolution, this map-based molecular structure will produce a high-quality atomic structure by interpreting them according to the atomic model. The positions in the electron density map are better when we use the atomic structure created from it. These positions can be defined as smaller than 1 Angstrom Å. In the lower resolution, we need to analyze more before using the final result. We have yet another limitation of the data obtained, that is, for the surface area and the unstable area of ​​the structure, the observed electron density maps are not clearly expressed, resulting in the structure corresponding only to the primary data, at the basic and the most accurate level possible. As we all know, atoms have their movements and depend heavily on temperature factors. It can be used to express the “chaotic” level of atoms. Moreover, so the temperature factor of the position of the atom in the structure model will provide good signs to evaluate each position of the atom. This temperature value covers the width of the Gaussian distribution curve of the model atom around the center of the atom. When this value is high (around 30), it shows the high degree of instability of the position of the analyzed atoms, the rhyme is further processed, and vice versa, this value is low (about 10), the location in the map is expressed [1].

Therefore, in order to implement this technique, we need to invest in equipping a qualified laboratory and equipment to carry out “raising” the crystal, collecting and processing X-ray data. There are many references available to this area that we can use for better understanding [3]. Another limitation of the X-ray crystallography method is the crystal requirement of the analytical structure [7]. The general structure may be the same when analyzing protein samples with different lattice structures. Besides, this requirement for many dissolved proteins cannot be met. Biological molecules are “forced” in a crystalline order, so the resulting structure is only a model that corresponds relatively well to biological molecules in nature. Therefore, the crystal structure needs

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