Spiegel M, Duraisamy A K, Schröder G F
Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany.
Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
J Struct Biol. 2015 Aug;191(2):207-13. doi: 10.1016/j.jsb.2015.06.007. Epub 2015 Jun 10.
Cryo-electron microscopy yields 3D density maps of macromolecules from single-particle images, tomograms, or 2D crystals. An optimal visualization of the density map is important for its proper interpretation. We have developed a method to improve the visualization of density maps by using general statistical information about proteins for the sharpening process. In particular, the packing density of atoms is highly similar between different proteins, which allows for building a pseudo-atomic model to approximate the true mass distribution. From this model the radial structure factor and density value histogram are estimated and applied as constraints to the 3D reconstruction in reciprocal- and real-space, respectively. Interestingly, similar improvements are obtained when using the correct radial structure factor and density value histogram from a crystal structure. Thus, the estimated pseudo-atomic model yields a sufficiently accurate mass distribution to optimally sharpen a density map.
冷冻电子显微镜可从单颗粒图像、断层扫描图或二维晶体生成大分子的三维密度图。密度图的最佳可视化对于其正确解读很重要。我们开发了一种方法，通过在锐化过程中使用关于蛋白质的一般统计信息来改善密度图的可视化。特别是，不同蛋白质之间原子的堆积密度高度相似，这使得能够构建一个伪原子模型来近似真实的质量分布。从这个模型中估计出径向结构因子和密度值直方图，并分别作为倒易空间和实空间中三维重建的约束条件。有趣的是，当使用来自晶体结构的正确径向结构因子和密度值直方图时，也能获得类似的改进。因此，估计出的伪原子模型产生了足够准确的质量分布，以最佳方式锐化密度图。
