scholarly journals Radiation decay of thaumatin crystals at three X-ray energies

2015 ◽  
Vol 71 (4) ◽  
pp. 772-778 ◽  
Author(s):  
Dorothee Liebschner ◽  
Gerold Rosenbaum ◽  
Miroslawa Dauter ◽  
Zbigniew Dauter
Keyword(s):  
Absorbed Dose ◽  
Protein Crystals ◽  
Average Intensity ◽  
Macromolecular Crystallography ◽  
Dose Limit ◽  
Initial Value ◽  
X Ray ◽  
Limit Value ◽  
Radiation Decay ◽  
Intensity Decay

Radiation damage is an unavoidable obstacle in X-ray crystallographic data collection for macromolecular structure determination, so it is important to know how much radiation a sample can endure before being degraded beyond an acceptable limit. In the literature, the threshold at which the average intensity of all recorded reflections decreases to a certain fraction of the initial value is called the `dose limit'. The first estimatedD50dose-limit value, at which the average diffracted intensity was reduced to 50%, was 20 MGy and was derived from observing sample decay in electron-diffraction experiments. A later X-ray study carried out at 100 K on ferritin protein crystals arrived at aD50of 43 MGy, and recommended an intensity reduction of protein reflections to 70%,D70, corresponding to an absorbed dose of 30 MGy, as a more appropriate limit for macromolecular crystallography. In the macromolecular crystallography community, the rate of intensity decay with dose was then assumed to be similar for all protein crystals. A series of diffraction images of cryocooled (100 K) thaumatin crystals at identical small, 2° rotation intervals were recorded at X-ray energies of 6.33 , 12.66 and 19.00 keV. Five crystals were used for each wavelength. The decay in the average diffraction intensity to 70% of the initial value, for data extending to 2.45 Å resolution, was determined to be about 7.5 MGy at 6.33 keV and about 11 MGy at the two higher energies.

scholarly journals Radiation protection x-ray in the diagnostic radiology unit kasih ibu kedonganan hospital

2019 ◽  
Vol 5 (6) ◽  
pp. 18-24
Author(s):  
I Ketut Putra ◽  
Ida Bagus Made Suryatika ◽  
I Gusti Agung Ayu Ratnawati ◽  
Gusti Ngurah Sutapa
Keyword(s):  
Radiation Exposure ◽  
Radiation Protection ◽  
General Public ◽  
Radiation Safety ◽  
Primary Wall ◽  
Dose Limit ◽  
X Ray ◽  
Limit Value ◽  
Room Design ◽  
Radiation Workers

One source of radiation is X-ray aircraft, which utilization must pay attention to safety aspects. Room design is the first step that must be done before the operation of X-ray aircraft. Radiology Unit Kasih Ibu Kedonganan Hospital operates an X-ray aircraft with specifications of 250 kV-85 mA, needs to be tested for radiation exposure which is an integral part of the verification of radiation protection. Test for radiation exposure at least once a year. The purpose of the installation room design is to ensure that workers or the general public around the plant receive radiation exposure that is smaller than the applicable dose limit value (DLV), by the radiation safety provisions that refer to the Decree. BAPETEN No. 7 of 2009 concerning Radiation Safety in the use of radiographic equipment. This study will test exposure to room wall shields associated with radiation workers and the general public. The results showed that all walls A, B, C, D, and E could still completely weaken the rate of X-ray radiation. The highest radiation dose detected on wall B is the primary wall for the Buky stand examination.

scholarly journals Visualization of protein crystals by high-energy phase-contrast X-ray imaging

2019 ◽  
Vol 75 (11) ◽  
pp. 947-958 ◽  
Author(s):  
Maxim Polikarpov ◽  
Gleb Bourenkov ◽  
Irina Snigireva ◽  
Anatoly Snigirev ◽  
Sophie Zimmermann ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Phase Contrast ◽  
High Energy ◽  
Protein Crystals ◽  
Cubic Phase ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Imaging

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallography beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

Influence of gamma irradiation on the surface morphology, XRD and thermophysical properties of silicide hexoboride

2018 ◽  
Vol 32 (14) ◽  
pp. 1850151 ◽  
Author(s):  
Matlab N. Mirzayev ◽  
Ravan N. Mehdiyeva ◽  
Ramin G. Garibov ◽  
Narmin A. Ismayilova ◽  
Sakin H. Jabarov
Keyword(s):  
Surface Morphology ◽  
Absorbed Dose ◽  
Radiation Absorption ◽  
X Ray Diffraction ◽  
Initial Value ◽  
Scanning Calorimetry ◽  
X Ray ◽  
Dose Rates ◽  
Spectrum Intensity ◽  
Dsc Method

In this study, compounds of B6Si were irradiated using a [Formula: see text]Co gamma source that have an energy line of 1.25 MeV at the absorbed dose rates from 14.6 kGy to 194.4 kGy. Surface morphology images of the sample obtained by Scanning Electron Microscope (SEM) show that the crystal structure at a high absorbed doses [Formula: see text] starts to be destroyed. X-ray diffraction studies revealed that with increasing radiation absorption dose, the spectrum intensity of the sample was decreased 1.96 times compared with the initial value. Thermal properties were studied by Differential scanning calorimetry (DSC) method in the temperature range of 30–1000[Formula: see text]C.

scholarly journals X-ray tomographic reconstruction and segmentation pipeline for the long-wavelength macromolecular crystallography beamline at Diamond Light Source

2021 ◽  
Vol 28 (3) ◽  
Author(s):  
Daniil Kazantsev ◽  
Ramona Duman ◽  
Armin Wagner ◽  
Vitaliy Mykhaylyk ◽  
Kazimir Wanelik ◽  
...  
Keyword(s):  
Light Source ◽  
Mother Liquor ◽  
Geodesic Distance ◽  
Computation Time ◽  
Gaussian Mixture ◽  
Protein Crystals ◽  
Macromolecular Crystallography ◽  
Low Contrast ◽  
X Ray ◽  
Long Wavelength

In this paper a practical solution for the reconstruction and segmentation of low-contrast X-ray tomographic data of protein crystals from the long-wavelength macromolecular crystallography beamline I23 at Diamond Light Source is provided. The resulting segmented data will provide the path lengths through both diffracting and non-diffracting materials as basis for analytical absorption corrections for X-ray diffraction data taken in the same sample environment ahead of the tomography experiment. X-ray tomography data from protein crystals can be difficult to analyse due to very low or absent contrast between the different materials: the crystal, the sample holder and the surrounding mother liquor. The proposed data processing pipeline consists of two major sequential operations: model-based iterative reconstruction to improve contrast and minimize the influence of noise and artefacts, followed by segmentation. The segmentation aims to partition the reconstructed data into four phases: the crystal, mother liquor, loop and vacuum. In this study three different semi-automated segmentation methods are experimented with by using Gaussian mixture models, geodesic distance thresholding and a novel morphological method, RegionGrow, implemented specifically for the task. The complete reconstruction-segmentation pipeline is integrated into the MPI-based data analysis and reconstruction framework Savu, which is used to reduce computation time through parallelization across a computing cluster and makes the developed methods easily accessible.

scholarly journals Exploiting fast detectors to enter a new dimension in room-temperature crystallography

2014 ◽  
Vol 70 (5) ◽  
pp. 1248-1256 ◽  
Author(s):  
Robin L. Owen ◽  
Neil Paterson ◽  
Danny Axford ◽  
Jun Aishima ◽  
Clemens Schulze-Briese ◽  
...  
Keyword(s):  
Simple Model ◽  
Data Collection ◽  
Room Temperature ◽  
Absorbed Dose ◽  
Temperature Data ◽  
Frame Rate ◽  
Protein Crystals ◽  
Lag Phase ◽  
First Time ◽  
Intensity Decay

A departure from a linear or an exponential intensity decay in the diffracting power of protein crystals as a function of absorbed dose is reported. The observation of a lag phase raises the possibility of collecting significantly more data from crystals held at room temperature before an intolerable intensity decay is reached. A simple model accounting for the form of the intensity decay is reintroduced and is applied for the first time to high frame-rate room-temperature data collection.

Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay

2009 ◽  
Vol 16 (2) ◽  
pp. 205-216 ◽  
Author(s):  
Adam I. Barker ◽  
Robert J. Southworth-Davies ◽  
Karthik S. Paithankar ◽  
Ian Carmichael ◽  
Elspeth F. Garman
Keyword(s):  
Room Temperature ◽  
Dose Dependence ◽  
Protein Crystals ◽  
Alternative Mechanism ◽  
X Ray ◽  
Dose Rates ◽  
Striking Change ◽  
Observed Damage ◽  
Dose Tolerance ◽  
Intensity Decay

The advent of highly intense wiggler and undulator beamlines has reintroduced the problem of X-ray radiation damage in protein crystals even at cryogenic temperatures (100 K). Although cryocrystallography can be utilized for the majority of protein crystals, certain macromolecular crystals (e.g. of viruses) suffer large increases in mosaicity upon flash cooling and data are still collected at room temperature (293 K). An alternative mechanism to cryocooling for prolonging crystal lifetime is the use of radioprotectants. These compounds are able to scavenge the free radical species formed upon X-ray irradiation which are thought to be responsible for part of the observed damage. Three putative radioprotectants, ascorbate, 1,4-benzoquinone and 2,2,6,6-tetramethyl-4-piperidone (TEMP), were tested for their ability to prolong lysozyme crystal lifetimes at 293 K. Plots of relative summed intensity against dose were used as a metric to assess radioprotectant ability: ascorbate and 1,4-benzoquinone appear to be effective, whereas studies on TEMP were inconclusive. Ascorbate, which scavenges OH^{\bullet} radicals (k OH = 8 × 109 M −1 s−1) and electrons with a lower rate constant (k e-(aq) = 3.0 × 108 M −1 s−1), doubled the crystal dose tolerance, whereas 1,4-benzoquinone, which also scavenges both OH^{\bullet} radicals (k OH = 1.2 × 109 M −1 s−1) and electrons (k e-(aq) = 1.2 × 1010 M −1 s−1), offered a ninefold increase in dose tolerance at the dose rates used. Pivotally, these preliminary results on a limited number of samples show that the two scavengers also induced a striking change in the dose dependence of the intensity decay from a first-order to a zeroth-order process.

Using image analysis for automated crystal positioning in a synchrotron X-ray beam for high-throughput macromolecular crystallography

2004 ◽  
Vol 37 (2) ◽  
pp. 265-269 ◽  
Author(s):  
Philippe Andrey ◽  
Bernard Lavault ◽  
Florent Cipriani ◽  
Yves Maurin
Keyword(s):  
Image Analysis ◽  
High Throughput ◽  
Protein Crystals ◽  
Structural Studies ◽  
Macromolecular Crystallography ◽  
Absolute Size ◽  
X Ray ◽  
X Ray Crystallography ◽  
Automated Method

A fully automated method for detecting and centring protein crystals for X-ray crystallography is described. It relies on the analysis of rotating crystal trace images. No assumption is made concerning the shape, absolute size, or position of the crystal within its holder. Crystals as small as 15 µm were successfully positioned. This represents an important step towards high-throughput structural studies.

scholarly journals Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE

2009 ◽  
Vol 16 (2) ◽  
pp. 152-162 ◽  
Author(s):  
Karthik S. Paithankar ◽  
Robin Leslie Owen ◽  
Elspeth F. Garman
Keyword(s):  
Absorbed Dose ◽  
Protein Crystal ◽  
Dose Calculations ◽  
Macromolecular Crystallography ◽  
Diffraction Intensity ◽  
Absorbed Energy ◽  
X Ray ◽  
Induced Changes ◽  
Acid Sample ◽  
Intensity Loss

Radiation damage is an unwelcome and unavoidable aspect of macromolecular crystallography. In order to quantify the extent of X-ray-induced changes, knowledge of the dose (absorbed energy per unit mass) is necessary since it is the obvious metric against which to plot variables such as diffraction intensity loss and B factors. Significant improvements to the program RADDOSE for accurately calculating the dose absorbed by macromolecular crystals are presented here. Specifically, the probability of energy loss through the escape of fluorescent photons from de-excitation of an atom following photoelectric absorption is now included. For lighter elements, both the probability of fluorescence and of its subsequent escape from the crystal are negligible, but for heavier atoms the chance of fluorescence becomes significant (e.g. 30% as opposed to Auger electron decay from a K-shell excited iron atom), and this has the effect of reducing the absorbed dose. The effects of this phenomenon on dose calculations are presented for examples of crystals of an iron-containing protein, 2-selenomethionine proteins, a uranium derivatised protein, and for a nucleic acid sample. For instance, the inclusion of fluorescent escape results in up to a 27% decrease in the calculated absorbed dose for a typical selenomethionine protein crystal irradiated at the selenium K-edge.

Dynamical Scattering in Electron Diffraction of wet Protein Crystals

1980 ◽  
Vol 38 ◽  
pp. 42-43
Author(s):  
B. B. Chang ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Scattering Theory ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Specimen Thickness ◽  
Major Question ◽  
X Ray ◽  
Scattering Effects ◽  
Diffraction Patterns ◽  
Acceleration Voltage

The significance of dynamical scattering effects remains the major question in the structural analysis by electron diffraction of protein crystals preserved in the hydrated state. In the few cases (single layers of purple membrane and 400-600 Å thick catalase crystals examined at 100 kV acceleration voltage) where electron-diffraction patterns were used quantitatively, dynamical scattering effects were considered unimportant on the basis of a comparison with x-ray intensities. The kinematical treatment is usually justified by the thinness of the crystal. A theoretical investigation by Ho et al. using Cowley-Moodie multislice formulation of dynamical scattering theory and cytochrome b5as the test object2 suggests that kinematical analysis of electron diffraction data with 100-keV electrons would not likely be valid for specimen thickness of 300 Å or more. We have chosen to work with electron diffraction patterns obtained from actual wet protein crystals (rat hemoglobin crystals of thickness range 1000 to 2500 Å) at 200 and 1000 kV and to analyze these for dynamical effects.

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