Qiangyan Pan

Automatic crystal centring procedure at the SSRF macromolecular crystallography beamline

X-ray diffraction is a common technique for determining crystal structures. The average time needed for the solution of a protein structure has been drastically reduced by a number of recent experimental and theoretical developments. Since high-throughput protein crystallography benefits from full automation of all steps that are carried out on a synchrotron beamline, an automatic crystal centring procedure is important for crystallographic beamlines. Fully automatic crystal alignment involves the application of optical methods to identify the crystal and move it onto the rotation axis and into the X-ray beam. Crystal recognition has complex dependencies on the illumination, crystal size and viewing angles due to effects such as local shading, inter-reflections and the presence of antifreezing elements. Here, a rapid procedure for crystal centring with multiple cameras using region segment thresholding is reported. Firstly, a simple illumination-invariant loop recognition and classification model is used by slicing a low-magnification loop image into small region segments, then classifying the loop into different types and aligning it to the beam position using feature vectors of the region segments. Secondly, an edge detection algorithm is used to find the crystal sample in a high-magnification image using region segment thresholding. Results show that this crystal centring method is extremely successful under fluctuating light states as well as for poorly frozen and opaque samples. Moreover, this crystal centring procedure is successfully integrated into the enhanced Blu-Ice data collection system at beamline BL17U1 at the Shanghai Synchrotron Radiation Facility as a routine method for an automatic crystal screening procedure.

A laser-Compton scattering prototype experiment at 100 MeV linac of Shanghai Institute of Applied Physics

As a prototype of the Shanghai Laser Electron Gamma Source in the Shanghai Synchrotron Radiation Facility, an x-ray source based on laser-Compton scattering (LCS) has been installed at the terminal of the 100 MeV linac of the Shanghai Institute of Applied Physics. LCS x-rays are generated by interactions between Q-switched Nd:yttrium aluminum garnet laser pulses [with wavelength of 1064 nm and pulse width of 21 ns (full width at half maximum)] and electron bunches [with energy of 108 MeV and pulse width of 0.95 ns (rms)] at an angle of 42 degrees between laser and electron beam. In order to measure the energy spectrum of LCS x-rays, a Si(Li) detector along the electron beam line axis is positioned at 9.8 m away from a LCS chamber. After background subtraction, the LCS x-ray spectrum with the peak energy of 29.1+/-4.4|(stat)+/-2.1|(syst) keV and the peak width (rms) of 7.8+/-2.8|(stat)+/-0.4|(syst) keV is observed. Normally the 100 MeV linac operates with the electron macropulse charge of 1.0 nC/pulse, and the electron and laser collision repetition rate of 20 Hz. Therefore, the total LCS x-ray flux of (5.2+/-2.0) x 10(2) Hz can be achieved.

A Future Laser Compton Scattering (LCS) γ-Ray Source: SLEGS at SSRF

The Shanghai Synchrotron Radiation Facility (SSRF) is a third-generation synchrotron radiation light source and will come into commission in April 2009. The project Shanghai Laser Electron Gamma Source (SLEGS), which is a high intensity γ-ray beamline based on Laser Compton Scattering (LCS) between relativistic electron bunches and a laser, has been proposed at the SSRF. According to our simulations, the SLEGS is expected to generate a polarized γ-ray beam of up to 22 MeV and 109–10 photons/s if using 3.5 GeV, 200–300 mA relativistic electrons and a 500 W CO2 polarized laser. Here we describe the status and the application prospects of SLEGS and its developed prototype.

Mini-beam modes on standard MX beamline BL17U at SSRF

The macromolecular crystallography beamlines at third-generation synchrotron facilities play a central role in solving macromolecular crystal structures and also in understanding the biological function at molecular levels. The MX beamline BL17U at Shanghai Synchrotron Radiation Facility is a typical standard MX beamline with a focused beam size (H × V) of FWHM around 80 μm × 45 μm. However the protein samples brought to the beamline are down to 5-10 m from the important and challenging science project now. These samples require smaller size beam. In order to achieve the mini-size beamline, two mini-beam modes have been developed on BL17U: the pinhole-based mini-beam and the focused mini-beam by compound refractive lens (CRL). Compared to the pinhole-based mode, three times increase in flux is obtained by the CRL mode at a similar beam size. The flux gain obtained by the CRL needs to be considered for data collection strategies. It takes few minutes to switch the beamline from the normal to CRL mini-beam mode.

Recognition of outer membrane proteins using adaptive neuro-fuzzy inference systems.

Recognition of outer membrane proteins (OMPs) from non-OMPs (global protein or inner protein) is one of the most important tasks in the field of computational biology and bioinformatics. Successful discrimination of OMPs from other types of proteins would help to identify new OMPs for biological applications. In this article, protein sequence index (PSI) and dipeptide motifs were applied to recognize OMPs from non-OMPs using adaptive neuro-fuzzy inference systems (ANFIS), results show that ANFIS can recognize OMPs from non-OMPs with high accuracy, and our method only depended on amino acid sequence.