scholarly journals TheLaueUtiltoolkit for Laue photocrystallography. I. Rapid orientation matrix determination for intermediate-size-unit-cell Laue data

2011 ◽  
Vol 44 (6) ◽  
pp. 1182-1189 ◽  
Author(s):  
Jarosław A. Kalinowski ◽  
Anna Makal ◽  
Philip Coppens
Keyword(s):  
Open Source ◽  
Unit Sphere ◽  
Reciprocal Lattice ◽  
Unit Cell ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Orientation Matrix ◽  
Intermediate Size

A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the experimental patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice with the corresponding pattern of a monochromatic data set on the same material. This technique is applied to the complete data set and thus eliminates problems often encountered when single frames with a limited number of peaks are to be used for orientation matrix determination. Application of the method to a series of Laue data sets on organometallic crystals is described. The corresponding program is available under a Mozilla Public License-like open-source license.

scholarly journals Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

2018 ◽  
Vol 74 (5) ◽  
pp. 411-421 ◽  
Author(s):  
Michael C. Thompson ◽  
Duilio Cascio ◽  
Todd O. Yeates
Keyword(s):  
Principal Component ◽  
Unit Cell ◽  
Protein Crystal ◽  
Data Sets ◽  
Structural Variations ◽  
Data Set ◽  
X Ray ◽  
Unit Cells ◽  
Factor Data ◽  
Dynamics Simulations

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

Determination of depth profiles from X-ray diffraction data

1993 ◽  
Vol 8 (2) ◽  
pp. 122-126 ◽  
Author(s):  
Paul Predecki
Keyword(s):  
Diffraction Data ◽  
Direct Method ◽  
Sample Surface ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Depth Profiles ◽  
A Direct Method

A direct method is described for determining depth profiles (z-profiles) of diffraction data from experimentally determined τ-profiles, where z is the depth beneath the sample surface and τ is the 1/e penetration depth of the X-ray beam. With certain assumptions, the relation between these two profile functions can be expressed in the form of a Laplace transform. The criteria for fitting experimental τ-data to functions which can be utilized by the method are described. The method was applied to two τ-data sets taken from the literature: (1) of residual strain in an A1 thin film and (2) of residual stress in a surface ground A12O3/5vol% TiC composite. For each data set, it was found that the z-profiles obtained were of two types: oscillatory and nonoscillatory. The nonoscillatory profiles appeared to be qualitatively consistent for a given data set. The oscillatory profiles were considered to be not physically realistic. For the data sets considered, the nonoscillatory z-profiles were found to lie consistently above the corresponding τ-profiles, and to approach the τ-profiles at large z, as expected from the relation between the two.

Determination of the distribution of elements with similar electron counts: a practical guide for resonant X-ray scattering

2013 ◽  
Vol 46 (3) ◽  
pp. 769-778 ◽  
Author(s):  
Simon Welzmiller ◽  
Philipp Urban ◽  
Felix Fahrnbauer ◽  
Loredana Erra ◽  
Oliver Oeckler
Keyword(s):  
Element Distribution ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
X Ray Scattering ◽  
Multiple Data ◽  
Straightforward Method ◽  
Distribution Of Elements ◽  
Ray Scattering

This article attempts to present straightforward and easy-to-understand guidelines for the determination of element distribution in compounds lacking X-ray scattering contrast because they have similar electron counts. Different sources of anomalous dispersion correction terms (especially Δf′ values) are compared with respect to their suitability, reliability and quality. Values from databases are compared with Δfvalues calculated from fluorescence spectra and those refined from single-crystal diffraction data, using both reference crystals without scattering contrast problems and crystals containing elements with similar electron counts. The number of data sets required to determine reliably the element distribution and the optimum wavelengths to be used are discussed. Joint multiple data set refinements are suitable for the refinement of multiply mixed occupancies of elements lacking scattering contrast. The most straightforward method of obtaining Δf′ values depends on the complexity of the problem to be solved and the precision required.

scholarly journals Determination of Acquisition Frequency for Intrafractional Motion of Pancreas in CyberKnife Radiotherapy

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Huailing Zhang ◽  
Guoru Zhao ◽  
David Djajaputra ◽  
Yaoqin Xie
Keyword(s):  
Effective Means ◽  
Time Interval ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Adequate Dose ◽  
Time Stamps ◽  
Movement Distance ◽  
Intrafractional Motion

Purpose.To report the characteristics of pancreas motion as tracked using implanted fiducials during radiotherapy treatments with CyberKnife.Methods and Materials. Twenty-nine patients with pancreas cancer treated using CyberKnife system were retrospectively selected for this study. During the treatment, the deviation is examined every 3-4 nodes (~45 s interval) and compensated by the robot. The pancreas displacement calculated from X-ray images acquired within the time interval between two consecutive couch motions constitute a data set.Results. A total of 498 data sets and 4302 time stamps of X-ray images were analyzed in this study. The average duration for each data set is 634 s. The location of the pancreas becomes more dispersed as the time elapses. The acquisition frequency depends on the prespecified movement distance threshold of pancreas. If the threshold between two consecutive images is 1 mm, the acquisition frequency should be less than 30 s, while if the threshold is 2 mm, the acquisition frequency can be around 1 min.Conclusions. The pancreas target moves significantly and unpredictably during treatment. Effective means of compensating the intrafractional movement is critical to ensure adequate dose coverage of the tumor target.

Crystallization and preliminary X-ray studies of sialidase L from the leech Macrobdella decora

1998 ◽  
Vol 54 (1) ◽  
pp. 111-113 ◽  
Author(s):  
Yu Luo ◽  
Min-yuan Chou ◽  
Su-chen Li ◽  
Yu-teh Li ◽  
Ming Luo
Keyword(s):  
Escherichia Coli ◽  
Unit Cell ◽  
Data Sets ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Mercury Derivative ◽  
Macrobdella Decora

Functional monomeric 83 kDa sialidase L, a NeuAcα2→3Gal-specific sialidase from Macrobdella leech, was expressed in Escherichia coli and readily crystallized by a macroseeding technique. The crystal belongs to space group P1 with unit-cell parameters a = 46.4, b = 69.3, c = 72.5 Å, α = 113.5, β = 95.4 and γ = 107.3°. There is one molecule per unit cell, giving a Vm = 2.4 Å3 Da−1 and a solvent content of 40%. Native and mercury-derivative data sets were collected to 2.0 Å resolution. Threading and molecular-replacement calculations confirmed the existence of a bacterial sialidase-like domain.

A batch-wise non-linear fitting and analysis tool for treating large X-ray diffraction data sets

2006 ◽  
Vol 39 (2) ◽  
pp. 262-266 ◽  
Author(s):  
R. J. Davies
Keyword(s):  
Diffraction Data ◽  
Operation Mode ◽  
Large Data ◽  
Scattering Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
X Ray ◽  
Linear Fitting ◽  
Non Linear

Synchrotron sources offer high-brilliance X-ray beams which are ideal for spatially and time-resolved studies. Large amounts of wide- and small-angle X-ray scattering data can now be generated rapidly, for example, during routine scanning experiments. Consequently, the analysis of the large data sets produced has become a complex and pressing issue. Even relatively simple analyses become difficult when a single data set can contain many thousands of individual diffraction patterns. This article reports on a new software application for the automated analysis of scattering intensity profiles. It is capable of batch-processing thousands of individual data files without user intervention. Diffraction data can be fitted using a combination of background functions and non-linear peak functions. To compliment the batch-wise operation mode, the software includes several specialist algorithms to ensure that the results obtained are reliable. These include peak-tracking, artefact removal, function elimination and spread-estimate fitting. Furthermore, as well as non-linear fitting, the software can calculate integrated intensities and selected orientation parameters.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

scholarly journals Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sites

2009 ◽  
Vol 42 (2) ◽  
pp. 259-264 ◽  
Author(s):  
Xinguo Hong ◽  
Quan Hao
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Unit Cell ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Molecular Envelope ◽  
Waxs Data ◽  
Ray Scattering

Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the programGASBORat 5 Å resolution (qmax= 1.25 Å−1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8 Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2σ level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax= 0.25 Å−1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination ofFSEARCHand WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement.

Über neue monocyclische Acyloxyfluoroborane 2.2.6.6-Tetrafluoro-1.4-dialkyl-1.3.5-trioxa-1.6-diboracyclohexene: Darstellung, Molekül- und Kristallstruktur/ New Monocyclic Acyloxyfluoroboranes 2,2,6,6-Tetrafluoro-1,4-dialkyl-1,3,5-trioxa-2,6-diboracyclohexenes: Synthesis, Molecular and Crystal Structure

1983 ◽  
Vol 38 (5) ◽  
pp. 554-558 ◽  
Author(s):  
Herbert Binder ◽  
Walter Matheis ◽  
Hans-Jörg Deiseroth ◽  
Han Fu-Son
Keyword(s):  
Crystal Structure ◽  
Organic Acid ◽  
Structure Determination ◽  
Unit Cell ◽  
Ring Conformation ◽  
X Ray ◽  
Conformational Isomers ◽  
Ring Group ◽  
Acid Anhydrides

Abstract Acyloxyfluoroboranes Trimeric alkoxydifluoroboranes (F2BOR)3 (2) react with organic acid anhydrides by substitution of a ring group OR forming monocyclic acyloxyfluoroboranes of the type 2,2,6,6-tetrafluoro-l,4-dialkyl-l,3,5-trioxa-2,6-diboracyclohexene (3). The X-ray crystal structure determination of 3a shows two conformational isomers: two planar and two non-planar six-membered rings are present in the unit cell. The ring conformation is influenced by weak intermolecular H — F interactions.

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