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IUCrJ

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https://www.readbyqxmd.com/read/30004094/response-to-comment-on-protein-crystal-lattices-are-dynamic-assemblies-the-role-of-conformational-entropy-in-the-protein-condensed-phase
#1
COMMENT
Margarita Dimova, Yancho D Devedjiev
A response is given to Nespolo's comment [ IUCrJ (2018), 5 , https://doi.org/10.1107/S2052252518006267] about the usage of the the term 'crystal lattice' in Dimova & Devedjiev [ IUCrJ (2018), 5 , 130-140].
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002853/erratum-grazing-incidence-small-angle-x-ray-scattering-gisaxs-on-small-periodic-targets-using-large-beams-erratum
#2
Mika Pflüger, Victor Soltwisch, Jürgen Probst, Frank Scholze, Michael Krumrey
[This corrects the article DOI: 10.1107/S2052252517006297.].
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002852/comment-on-the-article-protein-crystal-lattices-are-dynamic-assemblies-the-role-of-conformational-entropy-in-the-protein-condensed-phase
#3
COMMENT
Massimo Nespolo
A comment is given on Dimova & Devedjiev [ IUCrJ (2018), 5 , 130-140].
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002851/identification-of-a-tyrosine-switch-in-copper-haem-nitrite-reductases
#4
Jianshu Dong, Daisuke Sasaki, Robert R Eady, Svetlana V Antonyuk, S Samar Hasnain
There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase ( Rp NiR) with nitric oxide (NO) (-0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT 97...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002850/exploiting-superspace-to-clarify-vacancy-and-al-si-ordering-in-mullite
#5
Paul Benjamin Klar, Iñigo Etxebarria, Gotzon Madariaga
Synchrotron single-crystal X-ray diffraction has revealed diffuse scattering alongside sharp satellite reflections for different samples of mullite (Al4+2 x Si2-2 x O10- x ). Structural models have been developed in (3+1)-dimensional superspace that account for vacancy ordering and Al/Si ordering based on harmonic modulation functions. A constraint scheme is presented which explains the crystal-chemical relationships between the split sites of the average structure. The modulation amplitudes of the refinements differ significantly by a factor of ∼3, which is explained in terms of different degrees of ordering, i...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002849/structural-flexibility-of-halogen-bonds-showed-in-a-single-crystal-to-single-crystal-2-2-photodimerization
#6
Michael A Sinnwell, Jared N Blad, Logan R Thomas, Leonard R MacGillivray
Halogen bonds have emerged as noncovalent forces that govern the assembly of molecules in organic solids with a degree of reliability akin to hydrogen bonds. Although the structure-directing roles of halogen bonds are often compared to hydrogen bonds, general knowledge concerning the fundamental structural behavior of halogen bonds has had limited opportunity to develop. Following an investigation of solid-state reactions involving organic syntheses and the development of photoresponsive materials, this work demonstrates the ability of the components of intermolecular N⋯I halogen bonding - a 'workhorse' interaction for the crystal engineer - to support a single-crystal-to-single-crystal [2+2] photodimerization...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002848/structural-characterization-of-free-state-and-product-state-mycobacterium-tuberculosis-methionyl-trna-synthetase-reveals-an-induced-fit-ligand-recognition-mechanism
#7
Wei Wang, Bo Qin, Justyna Aleksandra Wojdyla, Meitian Wang, Xiaopan Gao, Sheng Cui
Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002847/sr-2-pt-8-x-as-a-layered-incommensurately-modulated-metal-with-saturated-resistivity
#8
Edoardo Martino, Alla Arakcheeva, Gabriel Autès, Andrea Pisoni, Maja D Bachmann, Kimberly A Modic, Toni Helm, Oleg V Yazyev, Philip J W Moll, László Forró, Sergiy Katrych
The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2 Pt8- x As, with x = 0.715 (5). The structure consists of Sr2 Pt3 As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002846/protonated-nucleobases-are-not-fully-ionized-in-their-chloride-salt-crystals-and-form-metastable-base-pairs-further-stabilized-by-the-surrounding-anions
#9
Prashant Kumar, Malgorzata Katarzyna Cabaj, Aleksandra Pazio, Paulina Maria Dominiak
This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies ( E es ) usually constitute 95% of the total interaction energy...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002845/chlamydia-protein-pgp3-studied-at-high-resolution-in-a-new-crystal-form
#10
Sahir Khurshid, Lata Govada, Gillian Wills, Myra O McClure, John R Helliwell, Naomi E Chayen
The protein Pgp3 is implicated in the sexually transmitted disease chlamydia and comprises an extended complex arrangement of a C-terminal domain (CTD) and an N-terminal domain (NTD) linked by a triple-helix coiled coil (THCC). Here, the X-ray crystal structure of Pgp3 from an LGV1 strain is reported at the highest X-ray diffraction resolution obtained to date for the full protein. The protein was crystallized using a high concentration of potassium bromide, which resulted in a new crystal form with relatively low solvent content that diffracted to a resolution of 1...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002844/towards-a-practical-implementation-of-x-ray-ghost-imaging-with-synchrotron-light
#11
Daniele Pelliccia, Margie P Olbinado, Alexander Rack, Andrew M Kingston, Glenn R Myers, David M Paganin
An experimental procedure for transmission X-ray ghost imaging using synchrotron light is presented. Hard X-rays from an undulator were divided by a beamsplitter to produce two copies of a speckled incident beam. Both beams were simultaneously measured on an indirect pixellated detector and the intensity correlation between the two copies was used to retrieve the ghost image of samples placed in one of the two beams, without measuring the samples directly. Aiming at future practical uses of X-ray ghost imaging, the authors discuss details regarding data acquisition, image reconstruction strategies and measure the point-spread function of the ghost-imaging system...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002843/monoclinic-distortion-polarization-rotation-and-piezoelectricity-in-the-ferroelectric-na-0-5-bi-0-5-tio-3
#12
Hyeokmin Choe, Johannes Bieker, Nan Zhang, Anthony Michael Glazer, Pam A Thomas, Semën Gorfman
The relationship between crystal structure and physical properties in the ferroelectric Na0.5 Bi0.5 TiO3 (NBT) has been of interest for the last two decades. Originally, the average structure was held to be of rhombohedral ( R 3 c ) symmetry with a fixed polarization direction. This has undergone a series of revisions, however, based on high-resolution X-ray diffraction, total neutron scattering, and optical and electron microscopy. The recent experimental findings suggest that the true average symmetry is monoclinic (space group Cc ), which allows for a rotatable spontaneous polarization...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002842/model-free-reconstruction-of-magnetic-correlations-in-frustrated-magnets
#13
Nikolaj Roth, Andrew F May, Feng Ye, Bryan C Chakoumakos, Bo Brummerstedt Iversen
Frustrated magnetic systems exhibit extraordinary physical properties, but quantification of their magnetic correlations poses a serious challenge to experiment and theory. Current insight into frustrated magnetic correlations relies on modelling techniques such as reverse Monte-Carlo methods, which require knowledge about the exact ordered atomic structure. Here, we present a method for direct reconstruction of magnetic correlations in frustrated magnets by three-dimensional difference pair distribution function analysis of neutron total scattering data...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002841/direct-shape-determination-of-intermediates-in-evolving-macromolecular-solutions-from-small-angle-scattering-data
#14
Petr V Konarev, Dmitri I Svergun
Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro . Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002840/dummy-atom-modelling-of-stacked-and-helical-nanostructures-from-solution-scattering-data
#15
Max Burian, Heinz Amenitsch
The availability of dummy-atom modelling programs to determine the shape of monodisperse globular particles from small-angle solution scattering data has led to outstanding scientific advances. However, there is no equivalent procedure that allows modelling of stacked, seemingly endless structures, such as helical systems. This work presents a bead-modelling algorithm that reconstructs the structural motif of helical and rod-like systems. The algorithm is based on a 'projection scheme': by exploiting the recurrent nature of stacked systems, such as helices, the full structure is reduced to a single building-block motif...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002839/using-cryo-electron-microscopy-maps-for-x-ray-structure-determination
#16
Lingxiao Zeng, Wei Ding, Quan Hao
X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002838/identification-of-ions-in-experimental-electrostatic-potential-maps
#17
Jimin Wang, Zheng Liu, Joachim Frank, Peter B Moore
Cryo-electron microscopy (cryo-EM) directly images the distribution of electrostatic potential (ESP) within macromolecules, and thus can provide much more information about atomic charge than X-ray crystallography. The electron-scattering length of an isolated ion is quite different from that of the corresponding neutral atom. The difference is very large at small scattering angles where the effects of electron distributions are largest, but becomes smaller at high scattering angles where nuclear charge determines outcomes...
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002837/symmetry-breaking-by-enzyme-catalyzed-epoxide-hydrolysis
#18
Christopher J Schofield
Janfalk Carlsson et al. [ IUCrJ (2018), 5 , 269-282] describe studies on factors determining selective ring opening of methylstyrene oxide stereoisomers by the epoxide hydrolase StEH1. The stereo-differentiating step is selective hydrolysis of an alkylated intermediate formed by reaction of the epoxide with an aspartyl residue.
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29755752/decoupling-anion-ordering-and-spin-peierls-transitions-in-a-strongly-one-dimensional-organic-conductor-with-a-chessboard-structure-o-me-2-ttf-2-no-3
#19
Olivier Jeannin, Eric W Reinheimer, Pascale Foury-Leylekian, Jean-Paul Pouget, Pascale Auban-Senzier, Elzbieta Trzop, Eric Collet, Marc Fourmigué
A mixed-valence conducting cation radical salt of the unsymmetrically substituted o -Me2 TTF donor molecule (TTF is tetrathiafulvalene) was obtained upon electrocrystallization in the presence of the non-centrosymmetric NO3 - anion. It crystallizes at room temperature in the monoclinic P 21 / c space group, with the anion disordered on an inversion centre. The donor molecules are stacked along the a axis. A 90° rotation of the longest molecular axis of o -Me2 TTF generates a chessboard-like structure, preventing lateral S⋯S contacts between stacks and providing a strongly one-dimensional electronic system, as confirmed by overlap interaction energies and band structure calculations...
May 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29755751/heterogeneous-local-order-in-self-assembled-nanoparticle-films-revealed-by-x-ray-cross-correlations
#20
Felix Lehmkühler, Florian Schulz, Martin A Schroer, Lara Frenzel, Holger Lange, Gerhard Grübel
We report on the self-assembly of gold nanoparticles coated with a soft poly(ethylene glycol) shell studied by X-ray cross-correlation analysis. Depending on the initial concentration of gold nanoparticles used, structurally heterogeneous films were formed. The films feature hot spots of dominating four- and sixfold local order with patch sizes of a few micrometres, containing 104 -105 particles. The amplitude of the order parameters suggested that a minimum sample amount was necessary to form well ordered local structures...
May 1, 2018: IUCrJ
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