On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps
On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps
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DOI：
10.1107/s0907444903026209
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发表时间：
2004-02-01
影响因子：
2.2
通讯作者：
Urzhumtsev, A
中科院分区：
文献类型：
--
作者：
Afonine, PV;Lunin, VY;Urzhumtsev, A
在过去的十年中，高分辨率的数据已经成为大分子物体。此外，超高分辨率衍射数据（分辨率接近0.6埃）已收集了几个蛋白质晶体。这允许研究电子密度分布的精细细节，例如变形密度，即实验确定的电子密度与由“自由”非键合原子组成的密度的偏差。本文讨论了在高分子的常规差分图中，使单个键处的价电子密度可见所必需的分辨率和原子温度因素。通过量子化学方法计算的理论地图的研究可以估计这些条件，这些结果通过分析亮氨酸脑啡肽和抗冻蛋白RD1的实验地图得到证实。发现接近0.6埃的分辨率极限对于细化是非常重要的，即使在较低分辨率下计算地图时也是如此。在接近0.9埃的分辨率下对相同模型的细化导致原子位移参数的值人为地增加，并且不允许在差异图中可见键电子密度。在一定程度上，原子位移参数的高估可能会受到限制，如果虚键电子在细化。
In the last decade, high-resolution data have become available for macromolecular objects. Furthermore, ultrahigh-resolution diffraction data (resolution close to 0.6 Angstrom) have been collected for several protein crystals. This allows the study of fine details of the electron-density distribution such as the deformation density, i.e. the deviation of the experimentally determined electron density from the density composed of 'free' non-bonded atoms. This paper discusses the resolution and atomic temperature factors necessary to make the valence electron density visible at individual bonds in conventional difference maps for macromolecules. The study of theoretical maps calculated by quantum-chemistry methods allows estimation of these conditions; these results are confirmed by analysis of experimental maps for Leu-enkephalin and antifreeze protein RD1. A resolution limit close to 0.6 Angstrom was found to be highly important for refinement even when the maps were calculated at lower resolution. The refinement of the same models at near to 0.9 Angstrom resolution results in artificially increased values of the atomic displacement parameters and does not permit bond electron density to be visible in difference maps. To some extent, overestimation of the atomic displacement parameters may be restricted if dummy bond electrons are used in the refinement.