Solution of the effects of twinning in femtosecond X-ray protein nanocrystallography

ZHOU Liang; LIU Peng; DONG Yu-Hui

doi:10.1088/1674-1137/37/2/028101

Chinese Physics C> 2013, Vol. 37> Issue(2) : 028101 DOI: 10.1088/1674-1137/37/2/028101

Solution of the effects of twinning in femtosecond X-ray protein nanocrystallography

Abstract
HTML
Reference
Related

PDF

Abstract：
With the development of the XFEL (X-ray free electron laser), high quality diffraction patterns from nanocrystals have been achieved. The nanocrystals with different sizes and random orientations are injected to the XFEL beams and the diffraction patterns can be obtained by the so-called "diffraction-and-destruction" mode. The recovery of orientations is one of the most critical steps in reconstructing the 3D structure of nanocrystals. There is already an approach to solve the orientation problem by using the automated indexing software in crystallography. However, this method cannot distinguish the twin orientations in the cases of the symmetries of Bravais lattices higher than the point groups. Here we propose a new method to solve this problem. The shape transforms of nanocrystals can be determined from all of the intensities around the diffraction spots, and then Fourier transformation of a single crystal cell is obtained. The actual orientations of the patterns can be solved by comparing the values of the Fourier transformations of the crystal cell on the intersections of all patterns. This so-called "multiple-common-line" method can distinguish the twin orientations in the XFEL diffraction patterns successfully.

References

[1]

Hajdu J. Current Opinion Structural Biology, 2000, 10: 569-573[2] Neutze R, Wouts R, Hajdu J et al. Nature, 2000, 406: 752-757[3] Caleman C, Huldt G, Ortiz C et al. ACS Nano, 2011, 5(1): 139-146[4] Chapman H N, Hajdu J, Spence J C H et al. Nature, 2011, 470: 73-77[5] Fienup J R. Appl. Opt., 1982, 21(15): 2758-2769[6] MIAO J, Ishikawa T, Anderson E H et al. Phys. Rev. B, 2003, 67(17): 174104[7] Spence J C H, Kirian R A, Chapman H N et al. Opt. Express, 2011, 19: 2866-2873[8] Kirian R A, Weierstall U, Spence J C H et al. Opt. Express, 2010, 18: 5713-5723[9] Leslie A G W. Acta Cryst. D, 2006, 62: 48-57[10] Kirian R A, White T A, Spence J C H et al. Acta Cryst. A, 2011, 67: 131-140[11] Huldt G, Szoke A, Hajdu J. Journal of Structural Biology, 2003, 144: 219-227[12] Shneerson V L, Ourmazd A, Saldin D K. Acta Cryst. A, 2008, 64: 303-315

[1]	Ran Huang , Yuan He , Zhi-Jun Wang , Wei-Ming Yue , An-Dong Wu , Yue Tao , Qiong Yang , Cong Zhang , Hong-Wei Zhao , Zhi-Hui Li . Analytical solution to the transient beam loading effects of a superconducting cavity. Chinese Physics C, 2017, 41(10): 107001. doi: 10.1088/1674-1137/41/10/107001
[2]	Mei-Qi Song , Qing-Min Zhang , Yu-Hang Guo , Kai Li , Hai-Xiao Deng . Numerical modeling of thermal loading of diamond crystal in X-ray FEL oscillators. Chinese Physics C, 2016, 40(4): 048101. doi: 10.1088/1674-1137/40/4/048101
[3]	LIU Long , HUANG Yang , XU Qing , YAN Ling-Tong , LI Li , FENG Song-Lin , FENG Xiang-Qian . Attenuation correction of L-shell X-ray fluorescence computed tomography imaging. Chinese Physics C, 2015, 39(3): 038203. doi: 10.1088/1674-1137/39/3/038203
[4]	LIU Guan-Fen , WANG We-Jia , XU Jia-Hua , DONG Yu-Hui . Small-angle X-ray scattering probe of intermolecularinteraction in red blood cells. Chinese Physics C, 2015, 39(3): 038001. doi: 10.1088/1674-1137/39/3/038001
[5]	FENG Zhao-Dong , JIANG Peng , ZHANG Hong-Kai , ZHAO Bo-Zhen , QIN Xiu-Bo , WEI Cun-Feng , LIU Yu , WEI Long . Performance assessment of CsI(Tl) screens on varioussubstrates for X-ray imaging. Chinese Physics C, 2015, 39(7): 078202. doi: 10.1088/1674-1137/39/7/078202
[6]	ZHOU Jian-Bin , LIU Yi , HONG Xu , ZHOU Jin , MA Ying-Jie , WANG Min , HU Yun-Chuan , CHEN Bao , YUE Ai-Zhong . Trapezoidal pulse shaping for pile-up pulse identification in X-ray spectrometry. Chinese Physics C, 2015, 39(6): 068201. doi: 10.1088/1674-1137/39/6/068201
[7]	ZHAO Bo-Zhen , QIN Xiu-Bo , FENG Zhao-Dong , WEI Cun-Feng , CHEN Yan , WANG Bao-Yi , WEI Long . Performance evaluation of CsI screens for X-ray imaging. Chinese Physics C, 2014, 38(11): 116003. doi: 10.1088/1674-1137/38/11/116003
[8]	SUN Li-Juan , CUI Ming-Qi , ZHU Jie , ZHAO Yi-Dong , ZHENG Lei , WANG Zhan-Shan , ZHU Jing-Tao . Multilayer-based soft X-ray polarimeter at the Beijing Synchrotron Radiation Facility. Chinese Physics C, 2013, 37(7): 078001. doi: 10.1088/1674-1137/37/7/078001
[9]	HUA Wen-Qiang , BIAN Feng-Gang , SONG Li , LI Xiu-Hong , WANG Jie . Hard X-ray optics simulation using the coherent mode decomposition of the Gaussian Schell model. Chinese Physics C, 2013, 37(6): 068001. doi: 10.1088/1674-1137/37/6/068001
[10]	YE Qing , CHEN Xing , ZHOU Jing , ZHAO Hai-Feng , CHU Wang-Sheng , ZHENG Xu-Sheng , WU Zi-Yu . Local hydrated structure of an Fe²⁺/Fe³⁺ aqueous solution: an investigation using a combination of molecular dynamics and X-ray absorption fine structure methods. Chinese Physics C, 2013, 37(3): 038003. doi: 10.1088/1674-1137/37/3/038003
[11]	WANG Yi , LI Qin , JIANG Xiao-Guo . Monte Carlo simulations for 20 MV X-ray spectrum reconstruction of a linear induction accelerator. Chinese Physics C, 2012, 36(9): 861-866. doi: 10.1088/1674-1137/36/9/012
[12]	LENG Yong-Bin , HUANG Guo-Qing , ZHANG Man-Zhou , CHEN Zhi-Chu , CHEN Jie , YE Kai-Rong . The beam-based calibration of an X-ray pinhole camera at SSRF. Chinese Physics C, 2012, 36(1): 80-83. doi: 10.1088/1674-1137/36/1/014
[13]	ZHANG Fei , WANG Huan-Yu , PENG Wen-Xi , LIANG Xiao-Hua , ZHANG Chun-Lei , CAO Xue-Lei , JIANG Wei-Chun , ZHANG Jia-Yu , CUI Xing-Zhu . High resolution solar soft X-ray spectrometer. Chinese Physics C, 2012, 36(2): 146-150. doi: 10.1088/1674-1137/36/2/008
[14]	DENG Biao , YANG Qun , XIE Hong-Lan , DU Guo-Hao , XIAO Ti-Qiao . First X-ray fluorescence CT experimental results at the SSRF X-ray imaging beamline. Chinese Physics C, 2011, 35(4): 402-404. doi: 10.1088/1674-1137/35/4/015
[15]	TAN Gao , WANG Hua-Qiao , CHEN Yu , YUAN Qing-Xi , LI Gang , ZHANG Xiao-Dan , ZHU Pei-Ping , ZHONG Xiu-Feng , TANG Jin-Tian . X-ray diffraction enhanced imaging study of intraocular tumors in human beings. Chinese Physics C, 2010, 34(2): 237-244. doi: 10.1088/1674-1137/34/2/016
[16]	XU Rui , LIU Chao-Pei . Instrumentation of coherent X-ray imaging and the primary experimental results. Chinese Physics C, 2010, 34(2): 224-226. doi: 10.1088/1674-1137/34/2/013
[17]	ZHOU Yi , LI Cheng , SUN Yong-Jie , SHAO Ming . An X-ray imaging device based on a GEM detector with delay-line readout. Chinese Physics C, 2010, 34(1): 78-82. doi: 10.1088/1674-1137/34/1/014
[18]	SHI Jia-Ru , CHEN Huai-Bi , TANG Chuan-Xiang , HUANG Wen-Hui , DU Ying-Chao , ZHENG Shu-Xin , REN Li . RF deflecting cavity for bunch length measurement in Tsinghua Thomson scattering X-ray source. Chinese Physics C, 2009, 33(S2): 161-164. doi: 10.1088/1674-1137/33/S2/042
[19]	LAN Ding , WANG Yu-Ren , ZHANG Yin-Min , WANG Wei , WU Zhong-Hua . Small angle X-ray scattering of the colloidal crystal. Chinese Physics C, 2009, 33(11): 1016-1018. doi: 10.1088/1674-1137/33/11/017
[20]	CHEN Miao-Xin , LI Zheng . Twin image removal in X-ray fluorescence holography with two energies. Chinese Physics C, 2008, 32(12): 1016-1020. doi: 10.1088/1674-1137/32/12/015

Access

Get Citation

ZHOU Liang, LIU Peng and DONG Yu-Hui. Solution of the effects of twinning in femtosecond X-ray protein nanocrystallography[J]. Chinese Physics C, 2013, 37(2): 028101. doi: 10.1088/1674-1137/37/2/028101

RIS(for EndNote,Reference Manager,ProCite)

BibTex

Txt

Milestone

Received: 2012-03-19
Revised: 2012-04-30

Article Metric

Article Views(2125)
PDF Downloads(277)
Cited by(0)

Policy on re-use

To reuse of subscription content published by CPC, the users need to request permission from CPC, unless the content was published under an Open Access license which automatically permits that type of reuse.

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Solution of the effects of twinning in femtosecond X-ray protein nanocrystallography

Corresponding author: DONG Yu-Hui,

Received Date: 2012-03-19

Accepted Date: 2012-04-30

Available Online: 2013-02-05

Abstract: With the development of the XFEL (X-ray free electron laser), high quality diffraction patterns from nanocrystals have been achieved. The nanocrystals with different sizes and random orientations are injected to the XFEL beams and the diffraction patterns can be obtained by the so-called "diffraction-and-destruction" mode. The recovery of orientations is one of the most critical steps in reconstructing the 3D structure of nanocrystals. There is already an approach to solve the orientation problem by using the automated indexing software in crystallography. However, this method cannot distinguish the twin orientations in the cases of the symmetries of Bravais lattices higher than the point groups. Here we propose a new method to solve this problem. The shape transforms of nanocrystals can be determined from all of the intensities around the diffraction spots, and then Fourier transformation of a single crystal cell is obtained. The actual orientations of the patterns can be solved by comparing the values of the Fourier transformations of the crystal cell on the intersections of all patterns. This so-called "multiple-common-line" method can distinguish the twin orientations in the XFEL diffraction patterns successfully.

HTML

Reference (1)

Solution of the effects of twinning in femtosecond X-ray protein nanocrystallography

Abstract：

References

Access

Article Metrics

Metrics

通讯作者: 陈斌, bchen63@163.com

Email This Article