Hegde Raghurama P, Fedorov Alexander A, Sauder J Michael, Burley Stephen K, Almo Steven C, Ramagopal Udupi A
Division of Biological Sciences, Poornaprajna Institute of Scientific Research, #4, 16th Cross, Sadashivnagar, Bangalore 560 080, India.
Department of Biochemistry, Albert Einstein College of Medicine, Ullmann Building, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA.
Acta Crystallogr F Struct Biol Commun. 2017 Apr 1;73(Pt 4):184-195. doi: 10.1107/S2053230X17002680. Epub 2017 Mar 22.
Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98 Å wavelength in one case and at 1.74 Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ∼1.0 Å wavelength, where the f'' value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structure de novo or in accurately assigning surface-bound atoms.
利用天然S原子或其他原子序数Z≤20的原子的反常信号进行的单波长反常色散(SAD),通常需要使用相对长波长的X射线收集高度冗余的数据。在此,展示了两种蛋白质的结果,其中利用偶然获得的表面结合Ca原子的反常信号(反常数据多重性约为10)来驱动从头结构测定。在这两种情况下,Ca原子均从结晶溶液中获得,并且数据收集策略并未针对利用这些散射体的反常信号进行优化。一种情况下,X射线数据在0.98 Å波长下收集,另一种情况在1.74 Å波长下收集(该波长是针对硫进行优化的,但利用钙的反常信号来解析结构)。同样,通过一个测试案例表明,在约1.0 Å波长下收集的数据(硫的f''值为0.28 e)足以使用来自强衍射晶体的固有S原子进行结构测定。有趣的是,还观察到SHELXD能够从高曝光数据中生成亚结构解,对于延伸至3.5 Å分辨率的低分辨率反射,其完整性为70%,且反常多重性相对较低。考虑到许多结晶条件中包含Cl、Ca、Mn等反常散射体这一事实,检查来自良好衍射晶体的数据中是否存在偶然的反常信号,对于从头确定结构或准确归属表面结合原子可能是有用的。