Fisher information for optimal planning of X-ray diffraction experiments

Fisher information is a powerful mathematical tool suitable for quantification of data `informativity' and optimization of the experimental setup and measurement conditions. Here, it is applied to X-ray diffraction and an informational approach to choosing the optimal measurement configuration is proposed. The core idea is maximization of the information which can be extracted from the measured data set by the selected analysis technique, over the sets of accessible reflections and measurement geometries. The developed approach is applied to high-resolution X-ray diffraction measurements and microstructure analysis of multilayer samples, and its efficiency and consistency are demonstrated with the results of more straightforward Monte Carlo simulations.

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Crystallization and preliminary X-ray diffraction analysis of Gos1p, a yeast SNARE protein

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14011704 ◽

2014 ◽

Vol 70 (7) ◽

pp. 967-969 ◽

Cited By ~ 3

Author(s):

Baoyun Cheng ◽

Yujie Zhang ◽

Gongrui Guo ◽

Yongxiang Gao

Keyword(s):

Snare Complex ◽

Receptor Complex ◽

Snare Protein ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

Data Set ◽

X Ray ◽

Cell Parameters ◽

The Core ◽

Endocytic Pathways

The Gos1 protein (Golgi SNAP receptor complex member 1) is involved in the SNARE complex, which is the core machinery that drives membrane fusion between cargo-carrying vesicles and their target membranes in the secretory and endocytic pathways in yeast. Truncated versions of the Gos1 protein fromSaccharomyces cerevisiaewere cloned, expressed, purified and crystallized. The crystal belonged to space groupP212121, with unit-cell parametersa= 39.67,b= 43.58,c= 81.94 Å, α = β = γ = 90°. An X-ray diffraction data set was collected at 100 K to 1.63 Å resolution. Matthews coefficient (VM) calculations suggest that one molecule is present in the asymmetric unit, corresponding to a solvent content of ∼55%.

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Purification, crystallization and preliminary X-ray diffraction analysis of the effector protein PevD1 fromVerticillium dahliae

Acta Crystallographica Section F Structural Biology and Crystallization Communications ◽

10.1107/s1744309112020556 ◽

2012 ◽

Vol 68 (7) ◽

pp. 802-805 ◽

Cited By ~ 4

Author(s):

Lei Han ◽

Zheng Liu ◽

Xinqi Liu ◽

Dewen Qiu

Keyword(s):

Pathogenic Fungus ◽

Sodium Formate ◽

Diffusion Method ◽

Effector Protein ◽

X Ray Diffraction ◽

Hanging Drop ◽

Dispersion Method ◽

Data Set ◽

X Ray ◽

Anomalous Signal

The effector protein PevD1 from the pathogenic fungusVerticillium dahliaewas purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals appeared in a solution consisting of 4.0 Msodium formate. A native data set was collected at 1.9 Å resolution at 100 K using an in-house X-ray source. Because of the absence of useful methinione in the protein sequence, derivative crystals that contained iodine were obtained by soaking in 1.25 Mpotassium iodide, and a data set that contained anomalous signal was collected using the same X-ray facility at a wavelength of 1.54 Å. The single-wavelength anomalous dispersion method was used to successfully solve the structure based on the anomalous signal generated from iodine.

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Unprecedented Hexa- and Undecanuclear Frameworks of Two New Tin(IV) Oxo Clusters Resulting from Partial Debenzylation Reactions

Zeitschrift für Naturforschung B ◽

10.1515/znb-2010-1101 ◽

2010 ◽

Vol 65 (11) ◽

pp. 1293-s1308 ◽

Cited By ~ 5

Author(s):

Laurent Plasseraud ◽

Hélène Cattey ◽

Philippe Richard

Keyword(s):

Solid State ◽

1H Nmr Spectroscopy ◽

Trifluoromethanesulfonic Acid ◽

Synthetic Route ◽

State Structure ◽

X Ray Diffraction ◽

Neutral Cluster ◽

Broad Resonance ◽

X Ray ◽

The Core

A new and facile synthetic route to the known neutral cluster ((PhCH2)2SnO)6[((PhCH2)2SnOH)2- (CO3)]2 (2) as well as its reactivity toward trifluoromethanesulfonic acid (HO3SCF3, TfOH) are reported. The solid-state structure of the new solvate 2·6C7H8 has been determined by single-crystal X-ray diffraction. The core of 2 can be described as a pair of coplanar pentanuclear [(PhCH2)2SnO]5 ladders bridged at their ends by two carbonate groups. Successive additions of TfOH to a suspension of 2 in CD3CN were monitored by 119Sn{1H} NMR spectroscopy showing the transformation of the fingerprint of 2 (δ = −244, −246, −306 ppm), via new upfield signals, to a final broad resonance located at δ = −474 ppm. Thereafter, two unprecedented ionic monobenzyltin(IV) oxo clusters, 3 and 4, resulting from a debenzylation reaction and exhibiting unusual hexa- and undecanuclear frameworks, respectively, have been isolated as single crystals.

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Crystallization and preliminary X-ray diffraction analysis of UspE fromEscherichia coli

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14023437 ◽

2014 ◽

Vol 70 (12) ◽

pp. 1640-1642 ◽

Cited By ~ 1

Author(s):

Yongbin Xu ◽

Chun-Shan Quan ◽

Xuanzhen Jin ◽

Xiaoling Jin ◽

Jing Zhao ◽

...

Keyword(s):

Stress Proteins ◽

Gel Filtration ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

Data Set ◽

X Ray ◽

Cell Parameters ◽

E Coli ◽

Vapour Diffusion ◽

Induced Genes

Universal stress proteins (Usps) are among the most highly induced genes when bacteria are subjected to several stress conditions such as heat shock, nutrient starvation or the presence of oxidants or other stress agents.Escherichia colihas five small Usps and one tandem-type Usp. UspE (or YdaA) is the tandem-type Usp and consists of two Usp domains arranged in tandem. To date, the structure of UspE remains to be elucidated. To contribute to the molecular understanding of the function of the tandem-type UspE, UspE fromE. coliwas overexpressed and the recombinant protein was purified using Ni–NTA affinity, Q anion-exchange and gel-filtration chromatography. Crystals of UspE were obtained by sitting-drop vapour diffusion. A diffraction data set was collected to a resolution of 3.2 Å from flash-cooled crystals. The crystals belonged to the tetragonal space groupI4122 orI4322, with unit-cell parametersa=b= 121.1,c = 241.7 Å.

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X-Ray Single Crystal Structural Analysis of Magnetically Oriented Microcrystals

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314088615 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1138-C1138

Author(s):

Chiaki Tsuboi ◽

Kazuki Aburaya ◽

Shingo Higuchi ◽

Fumiko Kimura ◽

Masataka Maeyama ◽

...

Keyword(s):

Molecular Structure ◽

Crystal Structure ◽

Single Crystal ◽

Three Dimensional ◽

Diffraction Measurement ◽

X Ray Diffraction ◽

Data Set ◽

Uv Curable ◽

X Ray

We have developed magnetically oriented microcrystal array (MOMA) technique that enables single crystal X-ray diffraction analyses from microcrystalline powder. In this method, microcrystals suspended in a UV-curable monomer matrix are there-dimensionally aligned by special rotating magnetic field, followed by consolidation of the matrix by photopolymerization. From thus achieved MOMAs, we have been succeeded in crystal structure analysis for some substances [1, 2]. Though MOMA method is an effective technique, it has some problems as follows: in a MOMA, the alignment is deteriorated during the consolidation process. In addition, the sample microcrystals cannot be recovered from a MOMA. To overcome these problems, we performed an in-situ X-ray diffraction measurement using a three-dimensional magnetically oriented microcrystal suspension (3D MOMS) of L-alanine. An experimental setting of the in-situ X-ray measurement of MOMS is schematically shown in the figure. L-alanine microcrystal suspension was poured into a glass capillary and placed on the rotating unit equipped with a pair of neodymium magnets. Rotating X-ray chopper with 10°-slits was placed between the collimator and the suspension. By using this chopper, it was possible to expose the X-ray only when the rotating MOMS makes a specific direction with respect to the impinging X-ray. This has the same effect as the omega oscillation in conventional single crystal measurement. A total of 22 XRD images of 10° increments from 0° to 220° were obtained. The data set was processed by using conventional software to obtain three-dimensional molecular structure of L-alanine. The structure is in good agreement with that reported for the single crystal. R1 and wR2 were 6.53 and 17.4 %, respectively. RMSD value between the determined molecular structure and the reported one was 0.0045 Å. From this result, we conclude that this method can be effective and practical to be used widely for crystal structure analyses.

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Centrosymmetric or Noncentrosymmetric? Case Study, Generalization and Structural Redetermination of Sr5Nb5O17

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768197019642 ◽

1998 ◽

Vol 54 (4) ◽

pp. 399-416 ◽

Cited By ~ 28

Author(s):

S. C. Abrahams ◽

H. W. Schmalle ◽

T. Williams ◽

A. Reller ◽

F. Lichtenberg ◽

...

Keyword(s):

Niobium Oxide ◽

The Novel ◽

Physical Measurement ◽

X Ray Diffraction ◽

Acta Cryst ◽

Data Set ◽

Space Group ◽

X Ray ◽

Atomic Coordinates

The possibility that the structure of the novel semiconducting perovskite-related material strontium niobium oxide, Sr5Nb5O17, refined by Schmalle et al. [Acta Cryst. (1995), C51, 1243–1246] in space group Pnn2, might instead belong to space group Pnnm has been investigated following an analysis of the atomic coordinates that indicated the latter space group to be more likely. All I obs were carefully remeasured, first those within a hemisphere containing c *, then all that lay within the full sphere of reflection. Refinement was undertaken, with each of two different sets of weights, in each space group. Each data set was used under three limiting intensity conditions: I obs > 4σ(I obs), I obs > 2σ(I obs) and finally with all reflections, but setting magnitudes with I obs ≤ 0 equal to 0. Fourteen separate tests based only upon the X-ray diffraction data may be used to distinguish between Pnn2 and Pnnm. Nine tests favored the latter choice, four were indeterminate and one was not used. Seven further tests may be made on the basis of physical measurement; of these, three strongly indicated Pnnm, one was indeterminate and three could not be used. The evidence clearly suggests the space group is Pnnm. The use of all reflections, including those with negative magnitude set equal to zero, is essential to avoid ambiguity in the X-ray diffraction tests and achieve the highest reliability. Refinement with weights based on variances of Type A and Type B [Schwarzenbach et al. (1995). Acta Cryst. A51, 565–569] resulted in improved reliability compared with that obtained from a popular empirical weighting scheme. The revised structure differs in several respects from that published previously.

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Cloning, expression, purification, crystallization and preliminary crystallographic analysis of 5-aminolaevulinic acid dehydratase fromBacillus subtilis

Acta Crystallographica Section F Structural Biology and Crystallization Communications ◽

10.1107/s1744309110027582 ◽

2010 ◽

Vol 66 (9) ◽

pp. 1053-1055 ◽

Cited By ~ 2

Author(s):

Qianda Lu ◽

Jinming Ma ◽

Hui Rong ◽

Jun Fan ◽

Ye Yuan ◽

...

Keyword(s):

Crystallographic Analysis ◽

Diffusion Method ◽

X Ray Diffraction ◽

Gene Encoding ◽

Data Set ◽

X Ray ◽

Aminolaevulinic Acid ◽

Acid Dehydratase ◽

Strain Bl21 ◽

Aminolaevulinic Acid Dehydratase

5-Aminolaevulinic acid dehydratase (ALAD), a crucial enzyme in the biosynthesis of tetrapyrrole, catalyses the condensation of two 5-aminolaevulinic acid (ALA) molecules to form porphobilinogen (PBG). The gene encoding ALAD was amplified from genomic DNA ofBacillus subtilisand the protein was overexpressed inEscherichia colistrain BL21 (DE3). The protein was purified and crystallized with an additional MGSSHHHHHHSSGLVPRGSH– tag at the N-terminus of the target protein. Diffraction-quality single crystals were obtained by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected at a resolution of 2.7 Å.

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Synthesis and Magnetic Properties of CoAl2O4 Coated Co Solid Solution Nanocapsules

Materials Science Forum ◽

10.4028/www.scientific.net/msf.663-665.1256 ◽

2010 ◽

Vol 663-665 ◽

pp. 1256-1259

Author(s):

Gui Mei Shi ◽

Ge Song ◽

Shu Lian ◽

Jin Bing Zhang

Keyword(s):

Solid Solution ◽

Photoelectron Spectrum ◽

Room Temperature ◽

Ferromagnetic State ◽

Antiferromagnetic Order ◽

X Ray Diffraction ◽

X Ray ◽

The Core ◽

New Type ◽

The Magnetic Field

A new type of antiferromagnetic CoAl2O4 coated ferromagnetic Co solid solution is synthesized by arc-discharging. Typical HRTEM images show that the nanocapsules form in a core-shell structure. The size of the nanocapsules is in range of 10-90 nm and the thickness of the shell is about 3-10 nm. X-ray photoelectron spectrum (XPS) and X-ray diffraction (XRD) reveal that the core consists of Co solid solution, while the shell is CoAl2O4. The magnetic field and temperature dependence of magnetizations confirm that the Co solid solution nanocapsules are basically in the ferromagnetic state below Curie temperature. In addition, the antiferromagnetic order occurs with Neél temperature TN of about 5 K. The saturation magnetization of Ms = 76.1 Am2/kg and the coercive force of Hc= 23.28 kA/m are achieved at room temperature for the Co solid solution nanocapsules.

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