O. Makarov

Radiation damage in protein crystals is reduced with a micron-sized X-ray beam

Radiation damage is a major limitation in crystallography of biological macromolecules, even for cryocooled samples, and is particularly acute in microdiffraction. For the X-ray energies most commonly used for protein crystallography at synchrotron sources, photoelectrons are the predominant source of radiation damage. If the beam size is small relative to the photoelectron path length, then the photoelectron may escape the beam footprint, resulting in less damage in the illuminated volume. Thus, it may be possible to exploit this phenomenon to reduce radiation-induced damage during data measurement for techniques such as diffraction, spectroscopy, and imaging that use X-rays to probe both crystalline and noncrystalline biological samples. In a systematic and direct experimental demonstration of reduced radiation damage in protein crystals with small beams, damage was measured as a function of micron-sized X-ray beams of decreasing dimensions. The damage rate normalized for dose was reduced by a factor of three from the largest (15.6 μm) to the smallest (0.84 μm) X-ray beam used. Radiation-induced damage to protein crystals was also mapped parallel and perpendicular to the polarization direction of an incident 1-μm X-ray beam. Damage was greatest at the beam center and decreased monotonically to zero at a distance of about 4 μm, establishing the range of photoelectrons. The observed damage is less anisotropic than photoelectron emission probability, consistent with photoelectron trajectory simulations. These experimental results provide the basis for data collection protocols to mitigate with micron-sized X-ray beams the effects of radiation damage.

The magnetic and diagnostics systems for the Advanced Photon Source self-amplified spontaneously emitting FEL

A self-amplified spontaneously emitting (SASE) free-electron laser (FEL) for the visible-to-ultraviolet spectral range is under construction at the Advanced Photon Source at Argonne National Laboratory. The amplifier part of the FEL consists of twelve identical 2.7-meter-long sections. Each section includes a 2.4-meter-long, 33-mm-period hybrid undulator, a quadruple lens, and a set of electron beam and radiation diagnostics equipment. The undulatory will operate at a fixed magnetic gap (approx. 9.3 mm) with K=3.1. The electron beam position will be monitored using capacitive beam position monitors, YAG scintillators with imaging optics, and secondary emission detectors. The spatial distribution of the photon beam will be monitored by position sensitive detectors equipped with narrow-band filters. A high-resolution spectrograph will be used to observe the spectral distribution of the FEL radiation.

JBluIce–EPICS control system for macromolecular crystallography

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline

Nonlinear optical (NLO) instrumentation has been integrated with synchrotron X-ray diffraction for combined single-platform analysis, examining the viability of NLO microscopy as an alternative to the conventional X-ray raster scan for the purposes of sample centering. Second-harmonic generation microscopy and two-photon excited ultraviolet fluorescence microscopy were evaluated for crystal detection, and assessed by X-ray raster scanning.

FEL development at the Advanced Photon Source

Construction of a single-pass free-electron laser (FEL) based on the self-amplified spontaneous emission (SASE) mode of operation is nearing completion at the Advanced Photon Source (APS) with initial experiments imminent. The APS SASE FEL is a proof-of-principle fourth-generation light source. As of January 1999 the undulator hall, end-station building, necessary transfer lines, electron and optical diagnostics, injectors, and initial undulators have been constructed and, with the exception of the undulators, installed. All preliminary code development and simulations have also been completed. The undulator hall is now ready to accept first beam for characterization of the output radiation. It is the project goal to push towards full FEL saturation, initially in the visible, but ultimately to UV and VUV, wavelengths.

Fast fluorescence techniques for crystallography beamlines.

This paper reports on several developments of X-ray fluorescence techniques for macromolecular crystallography recently implemented at the National Institute of General Medical Sciences and National Cancer Institute beamlines at the Advanced Photon Source. These include (i) three-band on-the-fly energy scanning around absorption edges with adaptive positioning of the fine-step band calculated from a coarse pass; (ii) on-the-fly X-ray fluorescence rastering over rectangular domains for locating small and invisible crystals with a shuttle-scanning option for increased speed; (iii) fluorescence rastering over user-specified multi-segmented polygons; and (iv) automatic signal optimization for reduced radiation damage of samples.

Micro‐Crystallography Developments at GM/CA‐CAT at the APS

Recently, several important structures have been solved using micro‐crystallographic techniques that previously could not have been solved with conventional crystallography. At GM/CA‐CAT we continue to develop micro‐crystallographic capabilities for difficult problems such as small crystals of large macromolecular complexes or membrane proteins grown in the lipidic cubic phase. This paper will describe three major upgrades to our arsenal of tools, “mini‐beam” collimators, active beamstop, and an improved goniostat. Our “mini‐beam” collimators have evolved to a new triple‐collimator fabricated from molybdenum as a uni‐body. This has significantly improved the robustness, ease of initial alignment, and reduction of background. More recently, two prototypes of a quad‐collimator have been developed and fabricated to provide a selection of mini‐beams of 5, 10, 20 μm and a 300 μm scatter‐guard on a single body. The smaller beams and samples have increased the demand on the tolerances of our goniostat. To meet t...

One‐Micron Beams for Macromolecular Crystallography at GM/CA‐CAT

GM/CA‐CAT has developed a 1‐μm beam for challenging micro‐diffraction experiments with macromolecular crystals (e.g. small crystals) and for radiation damage studies. Reflective (Kirkpatrick‐Baez mirrors) and diffractive (Fresnel zone plates) optics have been used to focus the beam. Both cases are constrained by the need to maintain a small beam convergence. Using two different zone plates, 1.0×1.0 and 0.8×0.9 μm2 (V×H,FWHM) beams were created at 15.2 keV and 18.5 keV, respectively. Additionally, by introducing a vertical focusing mirror upstream of the zone plate, a line focus at 15.2 keV was created (28×1.4 μm2 V×H,FWHM) with the line oriented perpendicular to the X‐ray polarization and the crystal rotation axis. Crystal‐mounting stages with nanometer resolution have been assembled to profile these beams and to perform diffraction experiments.

Radiometry based on synchrotron radiation from the storage ring VEPP-2M

Abstract Two experimental stations of the VEPP-2M storage ring are described in which calibrations of transfer standards, detectors, sources and a portable spectrometer are performed in the wavelength region 500–5500 A using synchrotron radiation as the primary standard.

Present status and recent results from the APS SASE FEL

The Low-Energy Undulator Test Line (LEUTL) at the Advanced Photon Source, Argonne National Laboratory, is intended to demonstrate the basic operation of a SASE-based free-electron laser. Goals include comparison of experimental results With theoretical predictions and scaling laws, identification of problems relevant to fourth-generation light source construction and operation and the means of addressing them, the development of operational and diagnostic techniques to optimize SASE FEL performance and increase repeatability from run to run. and performance of initial pioneering experiments capable of exploiting the unique properties of the laser. The basic layout and operational philosophy of the LEUTL experiment is presented. A summary of past results, including saturation, is reviewed, and a description of recent results is presented. We conclude with future plans, which include pressing to shorter wavelengths and incorporating user experiments into the LEUTL experimental program. (Less)