			Home About us Contact

Twin Fraction (twin + fraction)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Twinned crystals and anomalous phasing

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2003
Zbigniew Dauter
Merohedral or pseudomerohedral twinning of crystals cannot be identified from inspection of the diffraction patterns. Several methods for the identification of twinning and the estimation of the twin fraction are suitable for macromolecular crystals and all are based on the statistical properties of the measured diffraction intensities. If the crystal twin fraction is estimated and is not too close to 0.5, the diffraction data can be detwinned; that is, related to the individual crystal specimen. However, the detwinning procedure invariably introduces additional inaccuracies to the estimated intensities, which substantially increase when the twin fraction approaches 0.5. In some cases, a crystal structure can be solved with the original twinned data by standard techniques such as molecular replacement, multiple isomorphous replacement or multiwavelength anomalous diffraction. Test calculations on data collected from a twinned crystal of gpD, the bacteriophage , capsid protein, show that the single-wavelength anomalous diffraction (SAD) method can be used to solve its structure even if the data set corresponds to a perfectly twinned crystal with a twin fraction of 0.5. [source]

MIR phasing using merohedrally twinned crystals

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2003
Anke C. Terwisscha van Scheltinga
Merohedral twinning is a crystal-growth disorder that seriously hinders the determination of macromolecular crystal structures by isomorphous replacement. The strategies used in the structures solved so far are discussed. Several methods can be used to determine the extent of twinning, the twin fraction and to detwin the data. Accurate determination of the twin fraction by analysing heavy-atom refinement statistics is possible, but only influences the resulting phases slightly. It seems more crucial to restrict the variation in twin fractions between data sets, either by making the twin fractions of some data sets artificially higher or by screening crystals to obtain data with a low twin fraction. [source]

Crystallization and preliminary X-ray diffraction studies of a ferredoxin reductase component of carbazole 1,9a-dioxygenase from Novosphingobium sp.

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010

Carbazole 1,9a-dioxygenase (CARDO) is the initial enzyme of the carbazole-degradation pathway. The CARDO of Novosphingobium sp. KA1 consists of a terminal oxygenase, a putidaredoxin-type ferredoxin and a ferredoxin-NADH oxidoreductase (Red) and is classified as a class IIA Rieske oxygenase. Red from KA1 was crystallized at 278,K by the hanging-drop vapour-diffusion method using PEG 4000. The crystal diffracted to 1.58,Å resolution and belonged to space group P32, with unit-cell parameters a = b = 92.2, c = 78.6,Å, , = , = 90, , = 120°. Preliminary analysis of the X-ray diffraction data revealed that the asymmetric unit contained two Red monomers. The crystal appeared to be a merohedral twin, with a twin fraction of 0.32 and twin law (,h, ,k, l). [source]

Purification, crystallization and preliminary X-ray diffraction analysis of disease-related mutants of p97

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009
Wai-Kwan Tang
The human type II AAA+ protein p97 participates in various cellular activities, presumably through its involvement in the ubiquitin,proteasome degradation pathway. Mutations in p97 have been implicated in patients with inclusion-body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). In this work, three mutant p97 N-D1 fragments, R86A, R95G and R155H, were crystallized in the presence of ATP,S with PEG 3350 as a main precipitant, yielding two different crystal forms. The R155H mutant crystal belonged to space group R3, with unit-cell parameters in the hexagonal setting of a = b = 134.2, c = 182.9,Å, and was merohedrally twinned, with an estimated twin fraction of 0.34. The crystals of the R86A and R95G mutants belonged to space group P1, with similar unit-cell parameters of a = 90.89, b = 102.6, c = 107.2,Å, , = 97.5, , = 90.6, , = 91.5° and a = 92.76, b = 103.7, c = 107.7,Å, , = 97.7, , = 91.9, , = 89.7°, respectively. [source]

Expression, purification and crystallization of the ecto-enzymatic domain of rat E-NTPDase1 CD39

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2008
Xiaotian Zhong
CD39 is a prototype member of the ecto-nucleoside triphosphate diphosphohydrolase family that hydrolyzes extracellular nucleoside diphosphates and triphosphates in the presence of divalent cations. Here, the expression, purification and crystallization of the ecto-enzymatic domain of rat CD39, sCD39, are described. The 67,kDa secreted soluble glycoprotein was recombinantly overexpressed in a glycosylation mutant CHO line, Lec.3.2.8.1, and purified from conditioned media. Diffraction-quality crystals of sCD39 were produced by the vapor-diffusion method using PEG 3350 and ammonium dihydrogen phosphate as precipitants. The enzyme crystallized in a primitive trigonal form in space group P32, with unit-cell parameters a = b = 118.1, c = 81.6,Å and with two sCD39 copies in the asymmetric unit. Several low- to medium-resolution diffraction data sets were collected using an in-house X-ray source. Analysis of the intensity statistics showed that the crystals were invariably merohedrally twinned with a high twin fraction. For initial phasing, a molecular-replacement search was performed against the complete 3.2,Å data set using a maximum-likelihood molecular-replacement method as implemented in Phaser. The initial model of the two sCD39 monomers was placed into the P32 lattice and rigid-body refined and position-minimized with PHENIX. [source]

Expression, purification, crystallization and structure determination of two glutathione S -transferase-like proteins from Shewanella oneidensis

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2008
Bert Remmerie
Genome analysis of Shewanella oneidensis, a Gram-negative bacterium with an unusual repertoire of respiratory and redox capabilities, revealed the presence of six glutathione S -transferase-like genes (sogst1,sogst6). Glutathione S -transferases (GSTs; EC 2.5.1.18) are found in all kingdoms of life and are involved in phase II detoxification processes by catalyzing the nucleophilic attack of reduced glutathione on diverse electrophilic substrates, thereby decreasing their reactivity. Structure,function studies of prokaryotic GST-like proteins are surprisingly underrepresented in the scientific literature when compared with eukaryotic GSTs. Here, the production and purification of recombinant SoGST3 (SO_1576) and SoGST6 (SO_4697), two of the six GST-like proteins in S. oneidensis, are reported and preliminary crystallographic studies of crystals of the recombinant enzymes are presented. SoGST3 was crystallized in two different crystal forms in the presence of GSH and DTT that diffracted to high resolution: a primitive trigonal form in space group P31 that exhibited merohedral twinning with a high twin fraction and a primitive monoclinic form in space group P21. SoGST6 yielded primitive orthorhombic crystals in space group P212121 from which diffraction data could be collected to medium resolution after application of cryo-annealing protocols. Crystal structures of both SoGST3 and SoGST6 have been determined based on marginal search models by maximum-likelihood molecular replacement as implemented in the program Phaser. [source]

Nonmerohedrally twinned 6-amino-3-methyluracil-5-carbaldehyde: a hydrogen-bonded ribbon containing four types of ring

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2009
José M. de la Torre
In the title compound [systematic name: 6-amino-5-formyl-3-methylpyrimidine-2,4(1H,3H)-dione], C6H7N3O3, the intramolecular dimensions provide evidence for some polarization of the electronic structure. There is an intramolecular N,H...O hydrogen bond; this and a combination of three intermolecular N,H...O hydrogen bonds generate an almost planar ribbon containing S(6), R22(4), R21(6) and R44(16) rings. These ribbons are linked into sheets by a dipolar carbonyl,carbonyl interaction. The structure was refined as a nonmerohedral twin, with twin fractions 0.7924,(1) and 0.2076,(10). [source]

Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2009
Feng Yu
Human thymocyte nuclear protein 1 contains a unique DUF55 domain consisting of 167 residues (55,221), but its cellular function remains unclear. Crystals of DUF55 belonged to the trigonal space group P31, but twinning caused the data to approach apparent 622 symmetry. Two data sets were collected to 2.3,Å resolution. Statistical analysis confirmed that both data sets were partially twinned by tetartohedry. Tetartohedral twin fractions were estimated. After the structure had been determined, only one twofold axis of rotational pseudosymmetry was found in the crystal structure. Using the DALI program, a YTH domain, which is a potential RNA-binding domain from human YTH-domain-containing protein 2, was identified as having the most similar three-dimensional fold to that of DUF55. It is thus implied that DUF55 might be a potential RNA-related domain. [source]