Research On New Engineering Principle Of Single Crystal X-ray Diffraction Data Processing Of Biological Macromolecules

Crystal X-ray diffraction technology is the main technology for the structural analysis of biomacromolecules.The biomacromolecular diffraction beamlines relying on Shanghai Synchrotron Radiation Facility(SSRF)provide a strong support for the research of structural biology in China.However,at present,China doesn’t have its own crystal diffraction data processing software package,which can not fit the construction of radiation facilities.In order to better satisfy the needs of structural biology researchers for biomacromolecular diffraction data processing and reverse the long-term dependence on foreign software,our research group have comprehensively studied the main principles involved in single crystal X-ray diffraction data processing,and successfully processed the original diffraction images into standard crystallographic data including diffraction intensities and standard deviations marked by diffraction indices.This paper introduces the main scientific principles,engineering technical details and processing results of the basic modules involved in single crystal X-ray diffraction data processing developed by the author.It mainly includes:(1)Indexing:analyzing the geometric relationship involved in the diffraction experiment,using the full-space projection direction search and Fourier transform to analyze the crystal unit cell parameters and orientation,the principle of Niggli reduction,the judgment and transformation of the Bravais unit cell,the least square optimization of the reciprocal unit cell,Fourier transform of the difference vectors to calculate the coordinates of the incident beam center,and the correction of the crystal-to-detector distance.(2)Coordinate prediction:new definition of mosaicity to express the dispersion degree of the reciprocal-lattice spots,the simulation of the diffraction image under specified parameters,the prediction of the image coordinates of the diffraction spots by diffraction simulation,and the correction of predicted coordinates by the principle of homography transform.(3)Correction of intensities and standard deviations:scaling of the systemic response differences of intensities in different regions,using the normal probability plot to correct the standard deviations,and using Bayesian statistics to correct negative intensities.In the research process,the author has put forward some innovative methods,including:(1)A new method to automatically calculate the beam center coordinates using Fourier transform of the reciprocal difference vectors,which effectively solve the problem of missing beam centre of SSRF data.(2)A distance search optimization of the global error of reciprocal coordinates,which effectively solves the problem of large crystal-to-detector distance error of SSRF data.(3)Defining a new concept of mosaicity,which is described by the relative size of reciprocal diffraction spots and estimated automaticly,which can be self-consistently applied to the coordinate prediction simulation scheme.(4)The principle of homography transformation introduced for the first time to correct the deviation of the predicted image coordinates of the diffraction spots.(5)Three unique region-division schemes in scaling.These innovative methods effectively solve the problems of data from SSRF and improve the quality of data processing.For the modules with mature scientific principles,the author also gives feasible engineering schemes,designs effective logical frameworks and accumulates key engineering parameters.Finally,the programming language Python2 is used to complete the programming of each module of diffraction data processing,and a new single crystal X-ray processing software package autoPX has been integrated.These principles are verified by the processing of experimental diffraction data,whose results show that the structure analysis can be effectively completed by using the crystallographic data processed by autoPX.AutoPX has been installed and recommended by SSRF,which effectively supports the construction of biomacromolecular diffraction beamlines of synchrotron radiation facilities in China.