Molecular Biophysics and Integrated Bioimaging Department, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA.
Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 rue Laurent Fries, BP 10142, Illkirch, 67404, France.
Acta Crystallogr A Found Adv. 2023 Jul 1;79(Pt 4):345-352. doi: 10.1107/S205327332300356X. Epub 2023 Jun 20.
Diffraction intensities from a crystallographic experiment include contributions from the entire unit cell of the crystal: the macromolecule, the solvent around it and eventually other compounds. These contributions cannot typically be well described by an atomic model alone, i.e. using point scatterers. Indeed, entities such as disordered (bulk) solvent, semi-ordered solvent (e.g. lipid belts in membrane proteins, ligands, ion channels) and disordered polymer loops require other types of modeling than a collection of individual atoms. This results in the model structure factors containing multiple contributions. Most macromolecular applications assume two-component structure factors: one component arising from the atomic model and the second one describing the bulk solvent. A more accurate and detailed modeling of the disordered regions of the crystal will naturally require more than two components in the structure factors, which presents algorithmic and computational challenges. Here an efficient solution of this problem is proposed. All algorithms described in this work have been implemented in the computational crystallography toolbox (CCTBX) and are also available within Phenix software. These algorithms are rather general and do not use any assumptions about molecule type or size nor about those of its components.
大分子、周围的溶剂以及最终的其他化合物。这些贡献通常不能仅通过原子模型（即使用点散射体）很好地描述。事实上，诸如无序（主体）溶剂、半有序溶剂（例如膜蛋白中的脂质带、配体、离子通道）和无序聚合物环等实体需要比单个原子集合更复杂的建模。这导致模型结构因子包含多个贡献。大多数大分子应用程序假设双组分结构因子：一个组分来自原子模型，另一个组分描述主体溶剂。对晶体无序区域进行更准确和详细的建模自然需要结构因子中的两个以上的组分，这会带来算法和计算方面的挑战。本文提出了一种有效的解决方案。本工作中描述的所有算法都已在计算晶体学工具包 (CCTBX) 中实现，也可在 Phenix 软件中使用。这些算法非常通用，不使用关于分子类型或大小的任何假设，也不使用其组成部分的任何假设。
