scholarly journals NSLS-II MX beamlines FMX for micro-crystallography & AMX for highly automated MX

2014 ◽  
Vol 70 (a1) ◽  
pp. C1733-C1733
Author(s):  
Martin Fuchs ◽  
Robert Sweet ◽  
Lonny Berman ◽  
Dileep Bhogadi ◽  
Wayne Hendrickson ◽  
...  
Keyword(s):  
Energy Range ◽  
Structure Determination ◽  
Optical Systems ◽  
Photon Flux ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Binding Studies ◽  
X Ray ◽  
Array Detectors ◽  
Broad Energy Range

We present the final design of the x-ray optical systems and experimental stations of the two macromolecular crystallography (MX) beamlines, FMX and AMX, at the National Synchrotron Light Source-II (NSLS-II). Along with its companion x-ray scattering beamline, LIX, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX, [1]) will begin user operation in 2016. The pair of MX beamlines with complementary and overlapping capabilities is located at canted undulators (IVU21) in sector 17-ID. The Frontier Microfocusing Macromolecular Crystallography beamline (FMX) will deliver a photon flux of ~5x10^12 ph/s at a wavelength of 1 Å into a spot of 1 - 50 µm size. It will cover a broad energy range from 5 - 30 keV, corresponding to wavelengths from 0.4 - 2.5 Å. The highly Automated Macromolecular Crystallography beamline (AMX) will be optimized for high throughput applications, with beam sizes from 4 - 100 µm, an energy range of 5 - 18 keV (0.7 - 2.5 Å), and a flux at 1 Å of ~10^13 ph/s. Central components of the in-house-developed experimental stations are a 100 nm sphere of confusion goniometer with a horizontal axis, piezo-slits to provide dynamic beam size changes during diffraction experiments, a dedicated secondary goniometer for crystallization plates, and sample- and plate-changing robots. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and data collection of crystals in trays, for instance to characterize membrane protein crystals and to conduct ligand-binding studies. Together with the solution scattering program at LIX, the new beamlines will offer unique opportunities for advanced diffraction experiments with micro- and mini-beams, with next generation hybrid pixel array detectors and emerging crystal delivery methods such as acoustic droplet ejection. This work is supported by the US National Institutes of Health.

PROXIMA 2A: A New Micro-focus Beamline for Macromolecular Crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1672-C1672
Author(s):  
Denis Duran ◽  
Sebastien Le Couster ◽  
Gavin Fox ◽  
Roger Fourme ◽  
Rob Meijers ◽  
...  
Keyword(s):  
High Performance ◽  
Protein Structures ◽  
Photon Flux ◽  
First Year ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Fluorescence Detector ◽  
Beam Position ◽  
X Ray ◽  
Area Detector

PROXIMA 2A is a new micro-focus and energy tunable beamline dedicated to biological macromolecular crystallography at Synchrotron SOLEIL. The beamline officially opened in March 2013, and its first year of user operation has yielded excellent results. The X-ray source is a powerful in-vacuum U24 undulator coupled to a cryo-cooled Si[111] channel-cut monochromator and a pair of focussing bimorph mirrors in Kirpatrick-Baez configuration. This combination delivers a photon flux of over 10**12 ph/s into a focal spot of 10 μm × 5 μm (H×V FWHM), which is tunable over 6 – 15 keV. The supports of the optical elements have been designed to minimise the effects of vibrations and thermal dilations on the X-ray beam position, which is stable to within 5 microns over a day. The experimental station consists of a high performance micro-diffractometer, a cryostream, an area detector (ADSC Q315r), and an X-ray fluorescence detector. The X-ray energies for MAD experiments are directly calibrated on the sample. A robot equipped with a large 9 uni-puck dewar (CATS Irelec) is available to users for the automated transfer and screening of cryo-cooled samples. The users launch their experiments via an MXCuBE interface [1], which permits the centering of the sample, collecting of diffraction images, recording of X-ray spectra and the transfer of samples. The X-ray diffraction data are of an excellent quality, and the users readily exploit the micro-focused X-rays to select the best zones of their crystals. The first year of results from users has yielded a variety of success stories including novel protein structures resolved from crystals as small as 5 microns, as well as those solved by SAD & MAD methods. The future perspectives include automated helical and grid scans, in situ plate screening and multi-crystal merging techniques.

Performance of BL07A at NewSUBARU with installation of a new multi-layered-mirror monochromator

2021 ◽  
Vol 28 (2) ◽  
pp. 618-623
Author(s):  
Shotaro Tanaka ◽  
Shuto Suzuki ◽  
Tomohiro Mishima ◽  
Kazuhiro Kanda
Keyword(s):  
Synchrotron Radiation ◽  
Energy Range ◽  
Light Source ◽  
Monochromatic Light ◽  
High Vacuum ◽  
Photon Flux ◽  
X Rays ◽  
Monochromatic Beam ◽  
X Ray ◽  
High Photon Flux

Soft X-rays excite the inner shells of materials more efficiently than any other form of light. The investigation of synchrotron radiation (SR) processes using inner-shell excitation requires the beamline to supply a single-color and high-photon-flux light in the soft X-ray region. A new integrated computing multi-layered-mirror (MLM) monochromator was installed at beamline 07A (BL07A) of NewSUBARU, which has a 3 m undulator as a light source for irradiation experiments with high-photon-flux monochromatic light. The MLM monochromator has a high reflectivity index in the soft X-ray region; it eliminates unnecessary harmonic light from the undulator and lowers the temperature of the irradiated sample surfaces. The monochromator can be operated in a high vacuum, and three different mirror pairs are available for different experimental energy ranges; they can be exchanged without exposing the monochromator to the atmosphere. Measurements of the photon current of a photodiode on the sample stage indicated that the photon flux of the monochromatic beam was more than 1014 photons s−1 cm−2 in the energy range 80–400 eV and 1013 photons s−1 cm−2 in the energy range 400–800 eV. Thus, BL07A is capable of performing SR-stimulated process experiments.

Small-Angle X-ray Scattering at the ESRF High-Brilliance Beamline

1997 ◽  
Vol 30 (5) ◽  
pp. 867-871 ◽  
Author(s):  
P. Bösecke ◽  
O. Diat
Keyword(s):  
Small Angle ◽  
Small Angle Scattering ◽  
Optical Systems ◽  
Photon Flux ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Ray Scattering

The high-brilliance beamline (BL4/ID2) at the European Synchrotron Radiation Facility (ESRF) in Grenoble has been constructed with the emphasis on time-resolved small-angle X-ray scattering and macromolecular crystallography. It has been open to users for two years. The beamline has opened up new areas in small-angle scattering research, facilitating (a) small-angle crystallography on structures with unit cells of several hundredths of nanometres, (b) overlap with the light scattering range for the study of optical systems, (c) high photon flux for time-resolved experiments and (d) a high spatial coherence allowing submicrometre imaging with X-rays. The set-up and the detector system of the small-angle scattering station are presented. A method for obtaining absolute scattering intensities is described. The parasitic background at the station is discussed in terms of absolute scattering intensities.

scholarly journals Re-assessment of the Accretion Disc Clock in Hercules X-1

2010 ◽  
Vol 6 (S277) ◽  
pp. 325-328 ◽  
Author(s):  
E. Jurua ◽  
M. Still ◽  
P. J. Meintjes ◽  
P. A. Charles ◽  
S. K Anguma
Keyword(s):  
Neutron Star ◽  
Energy Range ◽  
Accretion Disc ◽  
X Rays ◽  
X Ray ◽  
Broad Energy Range ◽  
Sky Monitor ◽  
Broad Energy

AbstractThe Galactic neutron star X-ray binary Her X-1 shows a 35-day photometric modulation. Detected across a broad energy range, the modulation is prevalent in X-rays, cycling between low and high states. Since the discovery of the 35-day cycle of Her X-1, the X-ray source has entered and returned from an extended anomalous low state on at least seven occasions. Employing Rossi X-ray Timing Explorer All-Sky Monitor observations, prior predictions that Her X-1 would return from the 2003 - 2004 anomalous low state with a new precession period and accretion luminosity are verified. However, the precession has not been as coherent over recent years as predicted. Potentially there have been more minor anomalous low states between 2004 and the present day.

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 273 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals Determination of X-ray flux using silicon pin diodes

2009 ◽  
Vol 16 (2) ◽  
pp. 143-151 ◽  
Author(s):  
Robin L. Owen ◽  
James M. Holton ◽  
Clemens Schulze-Briese ◽  
Elspeth F. Garman
Keyword(s):  
Light Source ◽  
Energy Deposition ◽  
Photon Flux ◽  
Macromolecular Crystallography ◽  
Pin Diodes ◽  
Web Based ◽  
X Ray ◽  
Swiss Light Source ◽  
Flux Incident

Accurate measurement of photon flux from an X-ray source, a parameter required to calculate the dose absorbed by the sample, is not yet routinely available at macromolecular crystallography beamlines. The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV. These experiments have shown that a simple model based on energy deposition in silicon is sufficient for determining the flux incident on high-quality silicon pin diodes. The derivation and validation of this model is presented, and a web-based tool for the use of the macromolecular crystallography and wider synchrotron community is introduced.

scholarly journals A comprehensive Monte Carlo study to design a novel multi-nanoparticle loaded nanocomposites for augmentation of attenuation coefficient in the energy range of diagnostic X-rays

2021 ◽  
Vol 27 (4) ◽  
pp. 279-289
Author(s):  
Elahe Sayyadi ◽  
Asghar Mesbahi ◽  
Reza Eghdam Zamiri ◽  
Farshad Seyyed Nejad
Keyword(s):  
Monte Carlo ◽  
Energy Range ◽  
Radiation Protection ◽  
Experimental Studies ◽  
Rubber Matrix ◽  
Photon Flux ◽  
Monte Carlo Code ◽  
X Rays ◽  
Wide Range ◽  
Shielding Properties

Abstract Introduction: The present study aimed to investigate the radiation protection properties of silicon-based composites doped with nano-sized Bi2O3, PbO, Sm2O3, Gd2O3, WO3, and IrO2 particles. Radiation shielding properties of Sm2O3 and IrO2 nanoparticles were investigated for the first time in the current study. Material and methods: The MCNPX (2.7.0) Monte Carlo code was utilized to calculate the linear attenuation coefficients of single and multi-nano structured composites over the X-ray energy range of 10–140 keV. Homogenous distribution of spherical nanoparticles with a diameter of 100 nm in a silicon rubber matrix was simulated. The narrow beam geometry was used to calculate the photon flux after attenuation by designed nanocomposites. Results: Based on results obtained for single nanoparticle composites, three combinations of different nano-sized fillers Sm2O3+WO3+Bi2O3, Gd2O3+WO3+Bi2O3, and Sm2O3+WO3+PbO were selected, and their shielding properties were estimated. In the energy range of 20-60 keV Sm2O3 and Gd2O3 nanoparticles, in 70-100 keV energy range WO3 and for photons energy higher than 90 keV, PbO and Bi2O3 nanoparticles showed higher attenuation. Despite its higher density, IrO2 had lower attenuation compared to other nanocomposites. The results showed that the nanocomposite containing Sm2O3, WO3, and Bi2O3 nanoparticles provided better shielding among the studied samples. Conclusions: All studied multi-nanoparticle nanocomposites provided optimum shielding properties and almost 8% higher attenuation relative to single nano-based composites over a wide range of photon energy used in diagnostic radiology. Application of these new composites is recommended in radiation protection. Further experimental studies are suggested to validate our findings.

scholarly journals The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation

2019 ◽  
Vol 26 (3) ◽  
pp. 660-676 ◽  
Author(s):  
Adrian P. Mancuso ◽  
Andrew Aquila ◽  
Lewis Batchelor ◽  
Richard J. Bean ◽  
Johan Bielecki ◽  
...  
Keyword(s):  
Structure Determination ◽  
High Repetition Rate ◽  
Optical Systems ◽  
Diagnostic Tools ◽  
Imaging Method ◽  
Single Particles ◽  
X Ray ◽  
Data Rates ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation – in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

2018 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals The Role of Validation in Macromolecular Crystallography

1998 ◽  
Vol 54 (6) ◽  
pp. 1109-1118 ◽  
Author(s):  
Eleanor Dodson
Keyword(s):  
Structure Determination ◽  
Atomic Resolution ◽  
File Format ◽  
Macromolecular Crystallography ◽  
X Ray

The importance of validation techniques in X-ray structure determination and their relation to refinement procedures are discussed, with particular reference to atomic resolution structures. The requirements of deposition and publication, and the role of validation tools in this are analysed. The need for a rigorously defined file format is emphasized.

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