使用CCP4套件中的REFMAC5进行中子晶体学提炼.
Lucrezia Catapano1, Fei Long2, Keitaro Yamashita2
1Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom.
Acta crystallographica. Section D, Structural biology
|November 3, 2023
概括
中子晶体学现在可以使用增强的REFMAC5软件可视化宏分子中的大多数原子. 这种方法提高了结构精度,特别是对于质子化状态,克服了X射线结晶学的局限性.
科学领域:
- 结构生物学 结构生物学
- 生物物理学的生物物理.
- 计算生物学 计算生物学
背景情况:
- 原子对于宏分子功能至关重要,例如酶催化和蛋白质相互作用.
- 射线晶体学很难可视化大多数原子,这限制了对质子化状态的理解.
- 中子衍射,特别是用,有效地以常见分辨率可视化原子.
研究的目的:
- 扩展REFMAC5计划,使用中子晶体学数据来改进宏分子模型.
- 将精确的立体化学约束原子纳入CCP4单体图书馆.
- 引入和测试一种用于在中子衍射分析中提炼/分量的新特性.
主要方法:
- 扩展REFMAC5算法以处理中子晶体学数据.
- 在CCP4单体库中包含原子的立体化学限制.
- 开发用于中子散射的反/分数精炼参数.
- 在现有PDB条目和新结构 (FutA) 上测试增强的REFMAC5,单独使用中子数据或使用X射线限制.
主要成果:
- 使用增强的REFMAC5结构的重新精炼产生了与原始沉积物相比或更好的R因子值.
- 新加入的立体化学约束和反/分量的精细化提高了模型的准确性.
- 使用外部参考结构的限制被证明是有益的,特别是对于中低分辨率的结构.
结论:
- 扩展的REFMAC5程序有效地从中子结晶学数据中提炼宏分子模型.
- 这一进步有助于更准确地确定原子的位置和质子化状态.
- 由REFMAC5等增强的计算工具支持的中子晶体学是一种用于详细结构分析的强大方法.
相关概念视频
02:18X-ray Crystallography
The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
01:29Crystallographic Point Groups
Crystallographic point groups represent the various symmetry operations that can occur within crystals. They are unique in that at least one point will always remain unchanged during these actions. For instance, consider the triclinic system. This system, devoid of any axis or plane of symmetry, aligns with the C1 and Ci point groups.where Cᵢ is characterized solely by a center of inversion.Contrastingly, the monoclinic system introduces an element of symmetry. This system with one plane and...
01:29Determination of Crystal Structures
In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
01:25Imperfections in Crystal Structure: Point, Line and Plane Defects
A perfect crystal, in theory, has a uniform structure with the same unit cell and lattice points throughout. However, any deviation from this periodic arrangement is known as an imperfection or defect. These defects can be categorized into three types: point, line, and plane defects.Point defects occur when there is a deviation from the ideal due to missing atoms, displaced atoms, or additional atoms. These imperfections might occur due to imperfect packing during crystallization or because of...
01:26Imperfections in Crystal Structure: Stoichiometric Point Defects
Schottky defects arise when some lattice points in a crystal, such as those in NaCl, remain unoccupied, creating lattice vacancies without disturbing the overall electrical neutrality of the crystal. This defect is common in ionic crystals where the positive and negative ions are similar in size, as seen in sodium chloride and cesium chloride. The presence of Schottky defects enables the crystal to conduct electricity to a small extent through an ionic mechanism. Electric fields cause nearby...
01:29Imperfections in Crystal Structure: Non-Stoichiometric Defects
Non-stoichiometric defects refer to a type of defect in the crystal structure of a compound where the ratio of its constituent elements deviates from the ideal stoichiometric ratio. There are two main types of non-stoichiometric defects: metal excess defects and metal deficiency defects.Metal excess defects occur when there is a slight surplus of metal ions than what is required by the stoichiometric ratio of the compound. For example, heating a sodium chloride crystal in sodium vapor results...