scholarly journals Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips

2020 ◽  
Vol 76 (8) ◽  
pp. 751-758
Author(s):  
Jose A. Gavira ◽  
Isaac Rodriguez-Ruiz ◽  
Sergio Martinez-Rodriguez ◽  
Shibom Basu ◽  
Sébastien Teychené ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Room Temperature ◽  
Low Cost ◽  
Atomic Resolution ◽  
Microfluidic Channels ◽  
High Symmetry ◽  
X Ray ◽  
Counter Diffusion

Sample handling and manipulation for cryoprotection currently remain critical factors in X-ray structural determination. While several microchips for macromolecular crystallization have been proposed during the last two decades to partially overcome crystal-manipulation issues, increased background noise originating from the scattering of chip-fabrication materials has so far limited the attainable resolution of diffraction data. Here, the conception and use of low-cost, X-ray-transparent microchips for in situ crystallization and direct data collection, and structure determination at atomic resolution close to 1.0 Å, is presented. The chips are fabricated by a combination of either OSTEMER and Kapton or OSTEMER and Mylar materials for the implementation of counter-diffusion crystallization experiments. Both materials produce a sufficiently low scattering background to permit atomic resolution diffraction data collection at room temperature and the generation of 3D structural models of the tested model proteins lysozyme, thaumatin and glucose isomerase. Although the high symmetry of the three model protein crystals produced almost complete data sets at high resolution, the potential of in-line data merging and scaling of the multiple crystals grown along the microfluidic channels is also presented and discussed.

The structure of cubic MOF [{Ca(H2O)6}{CaGd(oxydiacetate)3}2].4H2O. A comparison between structural models obtained from Rietveld refinement of conventional and synchrotron X-ray powder diffraction data and standard refinement of single-crystal X-ray diffraction data

2012 ◽  
Vol 27 (4) ◽  
pp. 232-242 ◽  
Author(s):  
Leopoldo Suescun ◽  
Jun Wang ◽  
Ricardo Faccio ◽  
Guzmán Peinado ◽  
Julia Torres ◽  
...  
Keyword(s):  
Data Collection ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structural Models ◽  
Initial Time ◽  
High Symmetry ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

The structure of the metal–organic framework (MOF) compound [{Ca(H2O)6}{CaGd(oxydiacetate)3}2]·4H2O was determined by single-crystal X-ray diffraction and refined using conventional single-crystal X-ray diffraction data. In addition, the structure was refined using powder diffraction data collected from two sources, a conventional X-ray diffractometer in Bragg–Brentano geometry and a 12-detector high resolution synchrotron-based diffractometer in transmission geometry. Data from the latter were processed in three different ways to account for crystalline decay or radiation damage. One dataset was obtained by averaging the multiple detector patterns, another dataset was obtained by cutting the non-overlapping portions of each detector to consider only the first few minutes of data collection and a dose-corrected dataset was obtained by fitting the independent peaks in every dataset and extrapolating the intensity and peak position to the initial time of data collection or to zero-absorbed dose. The compared structural models obtained show that special processing of powder diffraction data produced a much accurate model, close to the single-crystal-based model for this particular compound with heavy atoms in high symmetry positions that do not contribute to a significant number of diffraction intensities.

Effects of NaBH4 Additions on Hydrogen Absorption by Nanostructured FeTi Powders

2008 ◽  
Vol 587-588 ◽  
pp. 921-925 ◽  
Author(s):  
Sofia F. Marques ◽  
Raquel A. Silva ◽  
Jose Brito Correia ◽  
Nobumitsu Shohoji ◽  
Carmen M. Rangel
Keyword(s):  
Hydrogen Absorption ◽  
Room Temperature ◽  
Elevated Temperatures ◽  
Low Cost ◽  
Reaction Products ◽  
X Ray Diffraction ◽  
X Ray ◽  
Gas Atmosphere ◽  
Scanning Electron

FeTi intermetallic powders are very promising media for reversible hydrogen storage. However, difficult activation treatments including annealing at elevated temperatures in high pressure H2 gas atmosphere are mandatory. In the present work nanostructured FeTi powders were produced and activated in situ at room temperature using mechanical alloying/milling (MA/MM) of pure metallic constituents, Fe and Ti, added with sodium borohydride. The resultant powders, FeTiHx, already H2 pre-charged, absorbed a significant amount of H2 but require optimization for reversible absorption/desorption. This system has one of the highest volumetric storage capacities and can be produced at low cost. Several parameters of the as-milled powders were controlled. The phase constitution of the reaction products was characterized by X-ray diffraction and scanning electron microscopy and the absorption isotherms of the activated powders were determined.

In situX-ray crystallography

2000 ◽  
Vol 33 (2) ◽  
pp. 397-400 ◽  
Author(s):  
Alexander McPherson
Keyword(s):  
Data Collection ◽  
Single Crystals ◽  
Room Temperature ◽  
Automated Data Collection ◽  
Vapor Diffusion ◽  
X Ray

A method is proposed, and preliminary experiments are described, for collection of X-ray data from macromolecular crystalsin situ. The usual processes of mounting for either room-temperature or cryogenic X-ray data collection are eliminated by growing crystals, using vapor diffusion, on small supports or films that can be either frozen or treated before transfer directly to the X-ray beam. The approach has the advantage that individual crystals are never manipulated and it is not necessary to isolate single crystals. Furthermore, crystals fixed to the surface on which they grow provides a positive advantage, small and otherwise problematic crystals become serviceable, and robotic or automated data collection becomes simplified.

scholarly journals An automated platform for in situ serial crystallography at room temperature

IUCrJ ◽  
2020 ◽  
Vol 7 (6) ◽  
pp. 1009-1018
Author(s):  
Zhong Ren ◽  
Cong Wang ◽  
Heewhan Shin ◽  
Sepalika Bandara ◽  
Indika Kumarapperuma ◽  
...  
Keyword(s):  
Data Collection ◽  
Room Temperature ◽  
Protein Structures ◽  
Routine Data ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
Serial Crystallography ◽  
Routine Data Collection

Direct observation of functional motions in protein structures is highly desirable for understanding how these nanomachineries of life operate at the molecular level. Because cryogenic temperatures are non-physiological and may prohibit or even alter protein structural dynamics, it is necessary to develop robust X-ray diffraction methods that enable routine data collection at room temperature. We recently reported a crystal-on-crystal device to facilitate in situ diffraction of protein crystals at room temperature devoid of any sample manipulation. Here an automated serial crystallography platform based on this crystal-on-crystal technology is presented. A hardware and software prototype has been implemented, and protocols have been established that allow users to image, recognize and rank hundreds to thousands of protein crystals grown on a chip in optical scanning mode prior to serial introduction of these crystals to an X-ray beam in a programmable and high-throughput manner. This platform has been tested extensively using fragile protein crystals. We demonstrate that with affordable sample consumption, this in situ serial crystallography technology could give rise to room-temperature protein structures of higher resolution and superior map quality for those protein crystals that encounter difficulties during freezing. This serial data collection platform is compatible with both monochromatic oscillation and Laue methods for X-ray diffraction and presents a widely applicable approach for static and dynamic crystallographic studies at room temperature.

scholarly journals High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions

2018 ◽  
Vol 13 (2) ◽  
pp. 260-292 ◽  
Author(s):  
Jana Broecker ◽  
Takefumi Morizumi ◽  
Wei-Lin Ou ◽  
Viviane Klingel ◽  
Anling Kuo ◽  
...  
Keyword(s):  
Data Collection ◽  
High Throughput ◽  
Room Temperature ◽  
Protein Crystals ◽  
X Ray ◽  
Cryogenic Conditions

High-throughput counter-diffusion capillary crystallization andin situdiffraction using high-pressure freezing in protein crystallography

2012 ◽  
Vol 45 (5) ◽  
pp. 999-1008 ◽  
Author(s):  
Mareike Kurz ◽  
Beat Blattmann ◽  
Andres Kaech ◽  
Christophe Briand ◽  
Paul Reardon ◽  
...  
Keyword(s):  
High Pressure ◽  
Low Temperature ◽  
Data Collection ◽  
High Throughput ◽  
Diffraction Data ◽  
High Throughput Screening ◽  
Structural Information ◽  
Major Step ◽  
Counter Diffusion

Post-crystallization treatments such as manual fishing of crystals and soaking in cryoprotectant solutions, especially of large macromolecular complexes and membrane proteins, are cumbersome and often lead to crystal damage and reduced diffraction data quality. Here, a capillary crystallization plate is presented that simultaneously allows counter-diffusion crystallization at the nanolitre scale in a high-throughput screening mode, low-temperaturein situdiffraction data collection from crystals after cryoprotection and low-temperaturein situdata collection of crystals without the addition of any cryoprotectant after high-pressure (HP) freezing. The development of this plate and plunge cooling of crystals in the capillaries is a major step towards implementing automatedin situhigh-throughput crystal diffraction data collection at a synchrotron beamline. In combination with HP freezing this offers a new opportunity to obtain structural information from fragile crystals of supramolecular complexes that might otherwise not be feasible.

Single Crystal Growth of High-Pressure Phases of Ice and Salt Hydrate Far Below the Original Melting Point by Mixing Alcohol: Crystal Structure Determination of Magnesium Chloride Heptahydrate

2020 ◽  
Author(s):  
Keishiro Yamashita ◽  
Kazuki Komatsu ◽  
Hiroyuki Kagi
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Crystal Growth ◽  
Single Crystal ◽  
Room Temperature ◽  
Growth Technique ◽  
Salt Hydrate ◽  
X Ray

An crystal-growth technique for single crystal x-ray structure analysis of high-pressure forms of hydrogen-bonded crystals is proposed. We used alcohol mixture (methanol: ethanol = 4:1 in volumetric ratio), which is a widely used pressure transmitting medium, inhibiting the nucleation and growth of unwanted crystals. In this paper, two kinds of single crystals which have not been obtained using a conventional experimental technique were obtained using this technique: ice VI at 1.99 GPa and MgCl<sub>2</sub>·7H<sub>2</sub>O at 2.50 GPa at room temperature. Here we first report the crystal structure of MgCl2·7H2O. This technique simultaneously meets the requirement of hydrostaticity for high-pressure experiments and has feasibility for further in-situ measurements.

Photoluminescence Enhancement of CdS Nanocrystals Fabricated on Dithiocarbamate Functionalized PET Substrates

2012 ◽  
Vol 512-515 ◽  
pp. 1511-1515
Author(s):  
Chun Lin Zhao ◽  
Li Xing ◽  
Xiao Hong Liang ◽  
Jun Hui Xiang ◽  
Fu Shi Zhang ◽  
...  
Keyword(s):  
Room Temperature ◽  
Hexagonal Structure ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Visible Absorption ◽  
X Ray ◽  
Cds Nanocrystals ◽  
Morphological Studies ◽  
Transmission Electron

Cadmium sulfide (CdS) nanocrystals (NCs) were self-assembled and in-situ immobilized on the dithiocarbamate (DTCs)-functionalized polyethylene glycol terephthalate (PET) substrates between the organic (carbon disulfide diffused in n-hexane) –aqueous (ethylenediamine and Cd2+ dissolved in water) interface at room temperature. Powder X-ray diffraction measurement revealed the hexagonal structure of CdS nanocrystals. Morphological studies performed by scanning electron microscopy (SEM) and high-resolution transmission electron microscope (HRTEM) showed the island-like structure of CdS nanocrystals on PET substrates, as well as energy-dispersive X-ray spectroscopy (EDS) confirmed the stoichiometries of CdS nanocrystals. The optical properties of DTCs modified CdS nanocrystals were thoroughly investigated by ultraviolet-visible absorption spectroscopy (UV-vis) and fluorescence spectroscopy. The as-prepared DTCs present intrinsic hydrophobicity and strong affinity for CdS nanocrystals.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

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