Afonine Pavel V, Mustyakimov Marat, Grosse-Kunstleve Ralf W, Moriarty Nigel W, Langan Paul, Adams Paul D
Lawrence Berkeley National Laboratory, Physical Biosciences Division, MS 64R0121, CA 94720, USA.
Acta Crystallogr D Biol Crystallogr. 2010 Nov;66(Pt 11):1153-63. doi: 10.1107/S0907444910026582. Epub 2010 Oct 20.
Approximately 85% of the structures deposited in the Protein Data Bank have been solved using X-ray crystallography, making it the leading method for three-dimensional structure determination of macromolecules. One of the limitations of the method is that the typical data quality (resolution) does not allow the direct determination of H-atom positions. Most hydrogen positions can be inferred from the positions of other atoms and therefore can be readily included into the structure model as a priori knowledge. However, this may not be the case in biologically active sites of macromolecules, where the presence and position of hydrogen is crucial to the enzymatic mechanism. This makes the application of neutron crystallography in biology particularly important, as H atoms can be clearly located in experimental neutron scattering density maps. Without exception, when a neutron structure is determined the corresponding X-ray structure is also known, making it possible to derive the complete structure using both data sets. Here, the implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described.
蛋白质数据库中约85%的结构是通过X射线晶体学解析出来的，这使其成为确定大分子三维结构的主要方法。该方法的局限性之一在于，典型的数据质量（分辨率）不允许直接确定氢原子的位置。大多数氢原子的位置可以从其他原子的位置推断出来，因此可以作为先验知识轻松纳入结构模型。然而，在大分子的生物活性位点可能并非如此，氢原子的存在和位置对酶促机制至关重要。这使得中子晶体学在生物学中的应用尤为重要，因为氢原子能够在实验中子散射密度图中清晰定位。无一例外，当确定了中子结构时，相应的X射线结构也已知，从而有可能利用这两个数据集推导完整的结构。在此，描述了在PHENIX系统中实施包含X射线和中子数据（单独或联合）的晶体学结构精修程序。
