Jelsch C, Pichon-Pesme V, Lecomte C, Aubry A
Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques (LCM3B), Université Henri Poincaré, Faculté des Sciences, CNRS UPRESA-7036, BP 239, 54506 Vandoeuvre-lès-Nancy CEDEX, France.
Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1306-18. doi: 10.1107/s0907444998004466.
Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 310 helix octapeptide Ac-Aib2-L-Lys(Bz)-Aib2-L-Lys(Bz)-Aib2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 A at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (DeltaB approximately 0.4 A2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 A2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 A.
亚原子分辨率的晶体学能够观察和测量电子密度（参数化为多极子）和原子电荷的非球形特征。通过应用电荷和多极子参数的可转移性概念，这种对电子密度的精细描述可以扩展到较低分辨率的结构。已经通过对几种肽晶体的电荷密度分析建立了这样一个参数数据库。本研究的目的是评估对于哪些X射线结构，可转移性的应用在物理上是有意义的。电荷密度多极子参数已被转移，随后对一种310螺旋八肽Ac-Aib2-L-Lys(Bz)-Aib2-L-Lys(Bz)-Aib2-NHMe的X射线结构进行了精修，该八肽在100K的低温下收集到了分辨率为0.82 Å的衍射数据。多极子转移导致晶体学残余因子wR和自由wR有显著改善。在变形电子密度图中，共价键和氧孤对中的电子积累在其预期值处清晰可见。对九种不同原子类型的电荷进行精修导致R因子进一步改善，并且精修后的电荷与AMBER分子建模字典中的电荷非常一致。使用根据电荷密度工作的平均结果计算的散射因子，八肽中原子坐标的位移可以忽略不计，但温度因子会发生显著变化（ΔB约为0.4 Ų）。在球形原子近似下，温度因子存在偏差，因为它们部分模拟了变形电子密度。因此，多极子的转移改善了热位移参数的物理意义。还分析了电子密度不同组分对衍射的贡献。该分析表明，当原子的热运动适中（B通常低于4 Ų）时，电子密度峰在动态变形图中定义良好。在这种情况下，变形密度的非截断傅里叶合成要求衍射数据的分辨率优于0.9 Å。
