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IUCrJ

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https://www.readbyqxmd.com/read/29354276/resolution-extension-by-image-summing-in-serial-femtosecond-crystallography-of-two-dimensional-membrane-protein-crystals
#1
Cecilia M Casadei, Ching-Ju Tsai, Anton Barty, Mark S Hunter, Nadia A Zatsepin, Celestino Padeste, Guido Capitani, W Henry Benner, Sébastien Boutet, Stefan P Hau-Riege, Christopher Kupitz, Marc Messerschmidt, John I Ogren, Tom Pardini, Kenneth J Rothschild, Leonardo Sala, Brent Segelke, Garth J Williams, James E Evans, Xiao-Dan Li, Matthew Coleman, Bill Pedrini, Matthias Frank
Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354275/active-site-solvent-replenishment-observed-during-human-carbonic-anhydrase-ii-catalysis
#2
Jin Kyun Kim, Carrie L Lomelino, Balendu Sankara Avvaru, Brian P Mahon, Robert McKenna, SangYoun Park, Chae Un Kim
Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO2/HCO3-. Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354274/crystal-structure-of-peroxiredoxin-3-from-vibrio-vulnificus-and-its-implications-for-scavenging-peroxides-and-nitric-oxide
#3
Jinsook Ahn, Kyung Ku Jang, Inseong Jo, Hasan Nurhasni, Jong Gyu Lim, Jin-Wook Yoo, Sang Ho Choi, Nam-Chul Ha
Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidase enzymes. Recently, a new type of Prx, VvPrx3, was identified in the pathogenic bacterium Vibrio vulnificus as being important for survival in macrophages. It employs only one catalytic cysteine residue to decompose peroxides. Here, crystal structures of VvPrx3 representing its reduced and oxidized states have been determined, together with an H2O2-bound structure, at high resolution. The crystal structure representing the reduced Prx3 showed a typical dimeric interface, called the A-type interface...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354273/local-scale-structures-across-the-morphotropic-phase-boundary-in-pbzr1-x-ti-x-o3
#4
Nan Zhang, Hiroko Yokota, A M Glazer, D A Keen, Semën Gorfman, P A Thomas, Wei Ren, Zuo-Guang Ye
Lead zirconate titanate (PZT) is one of the most widely studied piezoelectric materials, mainly because of its 'mysterious' relationship between the so-called morphotropic phase boundary (MPB) and its strong piezoelectric coupling factor. Using results from a pair distribution function analysis, this paper examines how the complex local structure in PZT affects the long-range average structure across the MPB. A monoclinic M C type structure is discovered in PZT. A first-order transformation between the monoclinic M A and M C components in both the average and local structures explains the sudden change in piezoelectric effect around these compositions...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354272/determination-of-atomic-vacancies-in-inas-gasb-strained-layer-superlattices-by-atomic-strain
#5
Honggyu Kim, Yifei Meng, Ji-Hwan Kwon, Jean-Luc Rouviére, Jian Min Zuo
Determining vacancy in complex crystals or nanostructures represents an outstanding crystallographic problem that has a large impact on technology, especially for semiconductors, where vacancies introduce defect levels and modify the electronic structure. However, vacancy is hard to locate and its structure is difficult to probe experimentally. Reported here are atomic vacancies in the InAs/GaSb strained-layer superlattice (SLS) determined by atomic-resolution strain mapping at picometre precision. It is shown that cation and anion vacancies in the InAs/GaSb SLS give rise to local lattice relaxations, especially the nearest atoms, which can be detected using a statistical method and confirmed by simulation...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354271/phase-transition-and-magnetocaloric-properties-of-mn50ni42-x-co-x-sn8-0-%C3%A2-x-%C3%A2-10-melt-spun-ribbons
#6
Zongbin Li, Yiwen Jiang, Zhenzhuang Li, César Fidel Sánchez Valdés, José Luis Sánchez Llamazares, Bo Yang, Yudong Zhang, Claude Esling, Xiang Zhao, Liang Zuo
The characteristics of magnetostructural coupling play a crucial role in the magnetic field-driven behaviour of magnetofunctional alloys. The availability of magnetostructural coupling over a broad temperature range is of great significance for scientific and technological purposes. This work demonstrates that strong magnetostrucural coupling can be achieved over a wide temperature range (222 to 355 K) in Co-doped high Mn-content Mn50Ni42-x Co x Sn8 (0 ≤ x ≤ 10) melt-spun ribbons. It is shown that, over a wide composition range with Co content from 3 to 9 at...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354270/snapshot-and-crystallographic-observations-of-kinetic-and-thermodynamic-products-for-no2s2-macrocyclic-complexes
#7
In-Hyeok Park, Yunji Kang, Eunji Lee, Huiyeong Ju, Seulgi Kim, Sujin Seo, Jong Hwa Jung, Shim Sung Lee
Direct observation and structural characterization of a kinetic product and a thermodynamic product for complexes with an NO2S2 macrocycle (L) are reported. L reacts with copper(I) iodide to give a mononuclear complex [Cu(L)]2(Cu2I4)·2CH2Cl2 (1), featuring three separate units. When cadmium(II) iodide was reacted with L, an anion-coordinated complex [Cd(L)I]2(Cd2I6)·4CH3CN (2) with a needle-type crystal shape was formed as the kinetic product. Interestingly, when the needle-type kinetic product was left undisturbed in the mother solution it gradually transformed to the pseudo-dimer complex [Cd2(L)2I2](Cd2I6) (3) with a brick-type crystal shape as the thermodynamic product...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354269/probing-the-accuracy-and-precision-of-hirshfeld-atom-refinement-with-hart-interfaced-with-olex2
#8
Malte Fugel, Dylan Jayatilaka, Emanuel Hupf, Jacob Overgaard, Venkatesha R Hathwar, Piero Macchi, Michael J Turner, Judith A K Howard, Oleg V Dolomanov, Horst Puschmann, Bo B Iversen, Hans-Beat Bürgi, Simon Grabowsky
Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element-hydrogen distances, r(X-H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X-H) values obtained from HAR...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354268/an-unprecedented-dioxygen-species-revealed-by-serial-femtosecond-rotation-crystallography-in-copper-nitrite-reductase
#9
Thomas P Halsted, Keitaro Yamashita, Kunio Hirata, Hideo Ago, Go Ueno, Takehiko Tosha, Robert R Eady, Svetlana V Antonyuk, Masaki Yamamoto, S Samar Hasnain
Synchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis. Using the newly developed approach of serial femtosecond rotation crystallography (SF-ROX), an X-ray damage-free structure of the as-isolated copper nitrite reductase (CuNiR) was visualized...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354267/building-inorganic-supramolecular-architectures-using-principles-adopted-from-the-organic-solid-state
#10
Marijana Đaković, Željka Soldin, Boris-Marko Kukovec, Ivan Kodrin, Christer B Aakeröy, Nea Baus, Tamara Rinkovec
In order to develop transferable and practical avenues for the assembly of coordination complexes into architectures with specific dimensionality, a strategy utilizing ligands capable of simultaneous metal coordination and self-complementary hydrogen bonding is presented. The three ligands used, 2(1H)-pyrazinone, 4(3H)-pyrimidinone and 4(3H)-quinazolinone, consistently deliver the required synthetic vectors in a series of CdII coordination polymers, allowing for reproducible supramolecular synthesis that is insensitive to the different steric and geometric demands from potentially disruptive counterions...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354266/hydrogen-bonds-in-crystalline-d-alanine-diffraction-and-spectroscopic-evidence-for-differences-between-enantiomers
#11
Ezequiel A Belo, Jose E M Pereira, Paulo T C Freire, Dimitri N Argyriou, Juergen Eckert, Heloisa N Bordallo
Enantiomeric amino acids have specific physiological functions in complex biological systems. Systematic studies focusing on the solid-state properties of d-amino acids are, however, still limited. To shed light on this field, structural and spectroscopic studies of d-alanine using neutron powder diffraction, polarized Raman scattering and ab initio calculations of harmonic vibrational frequencies were carried out. Clear changes in the number of vibrational modes are observed as a function of temperature, which can be directly connected to variations of the N-D bond lengths...
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354265/carbonic-anhydrase-under-pressure
#12
Anders Liljas
Investigations of the rapid enzyme carbonic anhydrase have now been extended by crystallographic analysis at high CO2 pressures to examine the movements of water molecules in different steps of the catalysis. The rate of catalysis seems well explained by the assembled observations.
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29354264/the-structural-science-of-functional-materials
#13
EDITORIAL
C Richard A Catlow
The growing complexity of functional materials and the major challenges this poses to structural science are discussed. The diversity of structural materials science and the contributions that computation is making to the field are highlighted.
January 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29123683/thermomechanical-effect-in-molecular-crystals-the-role-of-halogen-bonding-interactions
#14
Sudhir Mittapalli, D Sravanakumar Perumalla, Jagadeesh Babu Nanubolu, Ashwini Nangia
The design and synthesis of mechanically responsive materials is interesting because they are potential candidates to convert thermal energy into mechanical work. Reported in this paper are thermosalient effects in a series of halogen derivatives of salinazids. The chloro derivative, with higher electronegativity and a weaker inter-halogen bond strength (Cl⋯Cl) exhibits an excellent thermal response, whereas the response is weaker in the iodo derivative with stronger I⋯I halogen bonding. 3,5-Di-chloro-salinazid (Compound-A) exists in three polymorphic forms, two room-temperature polymorphs (Forms I and II) and one high-temperature modification (Form III)...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123682/analysis-of-xfel-serial-diffraction-data-from-individual-crystalline-fibrils
#15
David H Wojtas, Kartik Ayyer, Mengning Liang, Estelle Mossou, Filippo Romoli, Carolin Seuring, Kenneth R Beyerlein, Richard J Bean, Andrew J Morgan, Dominik Oberthuer, Holger Fleckenstein, Michael Heymann, Cornelius Gati, Oleksandr Yefanov, Miriam Barthelmess, Eirini Ornithopoulou, Lorenzo Galli, P Lourdu Xavier, Wai Li Ling, Matthias Frank, Chun Hong Yoon, Thomas A White, Saša Bajt, Anna Mitraki, Sebastien Boutet, Andrew Aquila, Anton Barty, V Trevor Forsyth, Henry N Chapman, Rick P Millane
Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123681/lifetimes-and-spatio-temporal-response-of-protein-crystals-in-intense-x-ray-microbeams
#16
Matthew A Warkentin, Hakan Atakisi, Jesse B Hopkins, Donald Walko, Robert E Thorne
Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s(-1). At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123680/hit-detection-in-serial-femtosecond-crystallography-using-x-ray-spectroscopy-of-plasma-emission
#17
H Olof Jönsson, Carl Caleman, Jakob Andreasson, Nicuşor Tîmneanu
Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123679/mix-and-diffuse-serial-synchrotron-crystallography
#18
Kenneth R Beyerlein, Dennis Dierksmeyer, Valerio Mariani, Manuela Kuhn, Iosifina Sarrou, Angelica Ottaviano, Salah Awel, Juraj Knoska, Silje Fuglerud, Olof Jönsson, Stephan Stern, Max O Wiedorn, Oleksandr Yefanov, Luigi Adriano, Richard Bean, Anja Burkhardt, Pontus Fischer, Michael Heymann, Daniel A Horke, Katharina E J Jungnickel, Elena Kovaleva, Olga Lorbeer, Markus Metz, Jan Meyer, Andrew Morgan, Kanupriya Pande, Saravanan Panneerselvam, Carolin Seuring, Aleksandra Tolstikova, Julia Lieske, Steve Aplin, Manfred Roessle, Thomas A White, Henry N Chapman, Alke Meents, Dominik Oberthuer
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123678/rare-earth-based-quaternary-heusler-compounds-mcovz-m-lu-y-z-si-ge-with-tunable-band-characteristics-for-potential-spintronic-applications
#19
Xiaotian Wang, Zhenxiang Cheng, Guodong Liu, Xuefang Dai, Rabah Khenata, Liying Wang, Abdelmadjid Bouhemadou
Magnetic Heusler compounds (MHCs) have recently attracted great attention since these types of material provide novel functionalities in spintronic and magneto-electronic devices. Among the MHCs, some compounds have been predicted to be spin-filter semiconductors [also called magnetic semiconductors (MSs)], spin-gapless semiconductors (SGSs) or half-metals (HMs). In this work, by means of first-principles calculations, it is demonstrated that rare earth-based equiatomic quaternary Heusler (EQH) compounds with the formula MCoVZ (M = Lu, Y; Z = Si, Ge) are new spin-filter semiconductors with total magnetic moments of 3 µB...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123677/in-vivo-analysis-of-the-escherichia-coli-ultrastructure-by-small-angle-scattering
#20
Enrico F Semeraro, Juliette M Devos, Lionel Porcar, V Trevor Forsyth, Theyencheri Narayanan
The flagellated Gram-negative bacterium Escherichia coli is one of the most studied microorganisms. Despite extensive studies as a model prokaryotic cell, the ultrastructure of the cell envelope at the nanometre scale has not been fully elucidated. Here, a detailed structural analysis of the bacterium using a combination of small-angle X-ray and neutron scattering (SAXS and SANS, respectively) and ultra-SAXS (USAXS) methods is presented. A multiscale structural model has been derived by incorporating well established concepts in soft-matter science such as a core-shell colloid for the cell body, a multilayer membrane for the cell wall and self-avoiding polymer chains for the flagella...
November 1, 2017: IUCrJ
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