scholarly journals Use of the Bruker AXS SMART BREEZE™ System for Macromolecular X-ray Data Collection

2016 ◽  
Vol 13 (4) ◽  
Author(s):  
Christiana Standle ◽  
Blake Overson ◽  
Cody Black ◽  
Guizella Rocabado ◽  
Bruce Howard
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Undergraduate Research ◽  
Inorganic Compounds ◽  
Copper Anode ◽  
X Ray Diffraction ◽  
Small Unit ◽  
X Ray ◽  
Unit Cells ◽  
Protein Enzyme

The Bruker AXS SMART BREEZE™ system is a single-crystal X-ray diffractometer designed to collect data from crystals of small organic or inorganic compounds. It is typically equipped with a Molybdenum-anode sealed tube to facilitate data collection from small unit cells. We recently acquired this system, but chose to have it installed with a copper-anode sealed tube with the hope of using it to collect data from larger unit cells such as those found in crystals of proteins or other macromolecules. This is the first and only BREEZE™ system installed by Bruker AXS with a copper-anode to date. Here we show that this system is capable of efficiently collecting quality X-ray diffraction data from crystals of the enzymes lysozyme and xylanase. This capability to collect diffraction data from both macromolecular and small-molecule crystals greatly expands the scope of undergraduate research projects that can be addressed using this instrument. KEYWORDS: X-ray; Diffraction; Crystallography; Diffractometer; Protein; Enzyme; Crystal; Structure

Powder X-ray diffraction of Metastudtite, (UO2)O2(H2O)2

2016 ◽  
Vol 31 (1) ◽  
pp. 71-72 ◽  
Author(s):  
Mark A. Rodriguez ◽  
Philippe E. Weck ◽  
Joshua D. Sugar ◽  
Thomas J. Kulp
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
First Principles ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Unit Cells

There has been some confusion in the published literature concerning the structure of Metastudtite (UO2)O2(H2O)2 where differing unit cells and space groups have been cited for this compound. Owing to the absence of a refined structure for Metastudtite, Weck et al. (2012) have documented a first-principles study of Metastudtite using density functional theory (DFT). Their model presents the structure of Metastudtite as an orthorhombic (space group Pnma) structure with lattice parameters of a = 8.45, b = 8.72, and c = 6.75 Å. A Powder Diffraction File (PDF) database entry has been allocated for this hypothetical Metastudtite phase based on the DFT modeling (see 01-081-9033) and aforementioned Dalton Trans. manuscript. We have obtained phase pure powder X-ray diffraction data for Metastudtite and have confirmed the model of Weck et al. via Rietveld refinement (see Figure 1). Structural refinement of this powder diffraction dataset has yielded updated refined parameters. The new cell has been determined as a = 8.411(1), b = 8.744(1), and c = 6.505(1) Å; cell volume = 478.39 Å3. There are only subtle differences between the refined structure and that of the first-principles model derived from DFT. Notably, the b-axis is significantly contracted in the final refinement as compared with DFT. There were also subtle changes to the U1, O1, and O3 atom positions. Tabulated powder diffraction data (d's and I's) for the Metastudtite have been derived from the refined model and these new values can serve to augment the PDF entry 01-081-9033 with a more updated entry based on observed X-ray powder diffraction data.

Masquerade: removing non-sample scattering from integrated reflection intensities

2012 ◽  
Vol 45 (2) ◽  
pp. 292-298 ◽  
Author(s):  
J. A. Coome ◽  
A. E. Goeta ◽  
J. A. K. Howard ◽  
M. R. Probert
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Low Temperatures ◽  
Test Case ◽  
X Rays ◽  
Atmospheric Conditions ◽  
X Ray Diffraction ◽  
New Approach ◽  
X Ray ◽  
Internal Agreement

X-ray diffraction experiments at very low temperatures require samples to be isolated from atmospheric conditions and held under vacuum. These conditions are usually maintainedviathe use of beryllium chambers, which also scatter X-rays, causing unwanted contamination of the sample's diffraction pattern. The removal of this contamination requires novel data-collection and processing procedures to be employed. Herein a new approach is described, which utilizes the differences in origin of scattering vectors from the sample and the beryllium to eliminate non-sample scattering. The programMasqueradehas been written to remove contaminated regions of the diffraction data from the processing programs. Coupled with experiments at different detector distances, it allows for the acquisition of decontaminated data. Studies of several single crystals have shown that this approach increases data quality, highlighted by the improvement in internal agreement factor with the test case of cytidine presented herein.

X-ray diffraction data and Rietveld refinement of CuGaxIn1-xSe2 (x=0.15 and 0.50)

2010 ◽  
Vol 25 (3) ◽  
pp. 253-257 ◽  
Author(s):  
E. J. Friedrich ◽  
R. Fernández-Ruiz ◽  
J. M. Merino ◽  
M. León
Keyword(s):  
Rietveld Refinement ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Zinc Blende ◽  
Metal Atoms ◽  
Tetragonal Crystal ◽  
Unit Cells ◽  
Type Crystal

X-ray powder diffraction data for CuGa0.15In0.85Se2 and CuGa0.50In0.50Se2 are reported. Indexing of the X-ray diffraction powder pattern and the Rietveld refinement confirmed that these compounds crystallize in the tetragonal crystal system, with space group I-42d (No. 122) and lattice parameters of a=5.7528(2) Å and c=11.5225(3) Å for CuGa0.15In0.85Se2 and a=5.6847(1) Å and c=11.2817(1) Å for CuGa0.50In0.50Se2. The CuGaxIn1−xSe2 system presents the chalcopyrite type crystal structure (CuFeS2) and corresponds to two stacked zinc-blende unit cells. The metal atoms Cu, In, and Ga are regularly ordered in the unit cell. Every Se atom is tetrahedrally bonded to two Cu and two In and Ga atoms.

scholarly journals The finer things in X-ray diffraction data collection

1999 ◽  
Vol 55 (10) ◽  
pp. 1718-1725 ◽  
Author(s):  
J. W. Pflugrath
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Rotation Angle ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Software Suite ◽  
X Ray ◽  
Position Sensitive ◽  
X Ray Background ◽  
Position Sensitive Detectors

X-ray diffraction images from two-dimensional position-sensitive detectors can be characterized as thick or thin, depending on whether the rotation-angle increment per image is greater than or less than the crystal mosaicity, respectively. The expectations and consequences of the processing of thick and thin images in terms of spatial overlap, saturated pixels, X-ray background andI/σ(I) are discussed. Thed*TREKsoftware suite for processing diffraction images is briefly introduced, and results fromd*TREKare compared with those from another popular package.

Unraveling the Structure of Decagonal Approximants by “Brute Force” Deconvolution of the Experimental Autocorrelation Function

2000 ◽  
Vol 643 ◽  
Author(s):  
Michael A. Estermann ◽  
Katja Lemster ◽  
Walter Steurer
Keyword(s):  
Autocorrelation Function ◽  
Diffraction Data ◽  
Brute Force ◽  
X Ray Diffraction ◽  
Large Unit ◽  
X Ray ◽  
Structure Building ◽  
Lack Of Information ◽  
Structure Solution ◽  
Unit Cells

AbstractMethods for the ab initio structure analysis of periodic approximant phases from single- crystal X-ray diffraction data are presented. These methods are particularly suited to complex approximant structures with large unit cells and strong pseudosymmetry (where routine X-ray structure solution tools fail) and are based on the “brute-force” deconvolution of the experimentally measured autocorrelation function. This function is obtained directly by a simple Fourier transform of the measured X-ray diffraction intensities. Sub-optimal diffraction data from twinned, nanodomain and polycrystalline specimens can be processed despite the inevitable lack of information due to reflection overlap and limited resolution. The deconvolution process allows complex approximant structures to be unraveled without prior knowledge about the structure-building motifs. Examples are presented for the systems Al-Co-Ni and Al-Co-(Ta).

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.

Influence of iron content on cell parameters of rhombohedral La0.6Sr0.4Co1−yFeyO3

1996 ◽  
Vol 11 (3) ◽  
pp. 240-245 ◽  
Author(s):  
Johan E. ten Elshof ◽  
Jaap Boeijsma
Keyword(s):  
Thermal Decomposition ◽  
Diffraction Data ◽  
Iron Content ◽  
Cell Parameter ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Unit Cells ◽  
Complex Solutions

Powder X-ray diffraction data are reported for La0.6Sr0.4Co1−yFeyO3 (y=0.1, 0.25, 0.4, 0.6, 0.8, 1.0). The powders were prepared by thermal decomposition of metal-containing complex solutions. All compositions have rhombohedral unit cells. In hexagonal setting, the cell parameters are a=5.4388 Å, c=13.2355 Å for y=0.1; a=5.4427 Å, c=13.2542 Å for y=0.25; a=5.4530 Å, c=13.2838 Å for y=0.4; a=5.4769 Å, c=13.3175 Å for y=0.6; a=5.5057 Å, c=13.3918 Å for y=0.8; and a=5.5278 Å, c=13.4368 Å for y=1.0. The space group is probably R3c (167) for all compositions. The observed trends in the change of the pseudocubic cell parameter ac with increasing iron content can be explained in terms of substitution of Co4+ by Fe4+ when y<0.4, and substitution of Co3+ by Fe3+ when y≳0.4.

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