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Sanchari Banerjee, Nathan P Coussens, François-Xavier Gallat, Nitish Sathyanarayanan, Jandhyam Srikanth, Koichiro J Yagi, James S S Gray, Stephen S Tobe, Barbara Stay, Leonard M G Chavas, Subramanian Ramaswamy
Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche...
July 1, 2016: IUCrJ
Sam Horrell, Svetlana V Antonyuk, Robert R Eady, S Samar Hasnain, Michael A Hough, Richard W Strange
Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1...
July 1, 2016: IUCrJ
Felix Simkovic, Jens M H Thomas, Ronan M Keegan, Martyn D Winn, Olga Mayans, Daniel J Rigden
For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer...
July 1, 2016: IUCrJ
Tsunetomo Yamada, Hiroyuki Takakura, Holger Euchner, Cesar Pay Gómez, Alexei Bosak, Pierre Fertey, Marc de Boissieu
The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom...
July 1, 2016: IUCrJ
Michael E Wall
Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods...
July 1, 2016: IUCrJ
Hakuba Kitagawa, Hiroyoshi Ohtsu, Aurora J Cruz-Cabeza, Masaki Kawano
The isolation and characterization of small sulfur allotropes have long remained unachievable because of their extreme lability. This study reports the first direct observation of disulfur (S2) with X-ray crystallography. Sulfur gas was kinetically trapped and frozen into the pores of two Cu-based porous coordination networks containing interactive iodide sites. Stabilization of S2 was achieved either through physisorption or chemisorption on iodide anions. One of the networks displayed shape selectivity for linear molecules only, therefore S2 was trapped and remained stable within the material at room temperature and higher...
July 1, 2016: IUCrJ
Tsutomu Ishimasa
Higher-dimensional structure analysis of quasicrystals is now possible. Yamada et al. [IUCrJ (2016), 3, 247-258] have solved the atomic structure of icosahedral ScZn7.33 including the characteristic imperfections.
July 1, 2016: IUCrJ
John Spence, Eaton Lattman
Serial crystallography at a synchrotron has been used to obtain time-resolved atomic resolution density maps of enzyme catalysis in copper nitrite reductase. Similar XFEL studies, intended to out-run radiation damage, will also soon appear.
July 1, 2016: IUCrJ
C Richard A Catlow
Articles published recently in IUCrJ continue to exemplify the developments and challenges in the structural science of materials.
July 1, 2016: IUCrJ
Matthias Burgener, Hanane Aboulfadl, Gaël Charles Labat, Michel Bonin, Martin Sommer, Ravish Sankolli, Michael Wübbenhorst, Jürg Hulliger
180° orientational disorder of molecular building blocks can lead to a peculiar spatial distribution of polar properties in molecular crystals. Here we present two examples [4-bromo-4'-nitrobiphenyl (BNBP) and 4-bromo-4'-cyanobiphenyl (BCNBP)] which develop into a bipolar final growth state. This means orientational disorder taking place at the crystal/nutrient interface produces domains of opposite average polarity for as-grown crystals. The spatial inhomogeneous distribution of polarity was investigated by scanning pyroelectric microscopy (SPEM), phase-sensitive second harmonic microscopy (PS-SHM) and selected volume X-ray diffraction (SVXD)...
May 1, 2016: IUCrJ
Ryohei Ishige, Gregory A Williams, Yuji Higaki, Noboru Ohta, Masugu Sato, Atsushi Takahara, Zhibin Guan
A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11-1] plane aligned nearly parallel to the film surface in the initial state...
May 1, 2016: IUCrJ
I L Shul'pina, I A Prokhorov, Yu A Serebryakov, I Zh Bezbakh
The authors' experience of the application of X-ray diffraction imaging in carrying out space technological experiments on semiconductor crystal growth for the former USSR and for Russia is reported, from the Apollo-Soyuz programme (1975) up to the present day. X-ray topography was applied to examine defects in crystals in order to obtain information on the crystallization conditions and also on their changes under the influence of factors of orbital flight in space vehicles. The data obtained have promoted a deeper understanding of the conditions and mechanisms of crystallization under both microgravity and terrestrial conditions, and have enabled the elaboration of terrestrial methods of highly perfect crystal growth...
May 1, 2016: IUCrJ
Helen E Maynard-Casely, Robert Hodyss, Morgan L Cable, Tuan Hoang Vu, Martin Rahm
Using synchrotron X-ray powder diffraction, the structure of a co-crystal between benzene and ethane formed in situ at cryogenic conditions has been determined, and validated using dispersion-corrected density functional theory calculations. The structure comprises a lattice of benzene molecules hosting ethane molecules within channels. Similarity between the intermolecular interactions found in the co-crystal and in pure benzene indicate that the C-H⋯π network of benzene is maintained in the co-crystal, however, this expands to accommodate the guest ethane molecules...
May 1, 2016: IUCrJ
Karol Nass, Anton Meinhart, Thomas R M Barends, Lutz Foucar, Alexander Gorel, Andrew Aquila, Sabine Botha, R Bruce Doak, Jason Koglin, Mengning Liang, Robert L Shoeman, Garth Williams, Sebastien Boutet, Ilme Schlichting
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms...
May 1, 2016: IUCrJ
Jack Binns, Konstantin V Kamenev, Garry J McIntyre, Stephen A Moggach, Simon Parsons
The first high-pressure neutron diffraction study in a miniature diamond-anvil cell of a single crystal of size typical for X-ray diffraction is reported. This is made possible by modern Laue diffraction using a large solid-angle image-plate detector. An unexpected finding is that even reflections whose diffracted beams pass through the cell body are reliably observed, albeit with some attenuation. The cell body does limit the range of usable incident angles, but the crystallographic completeness for a high-symmetry unit cell is only slightly less than for a data collection without the cell...
May 1, 2016: IUCrJ
Jerome de Ruyck, Marc F Lensink, Julie Bouckaert
Selective inhibitors of the type 1 fimbrial adhesin FimH are recognized as attractive alternatives for antibiotic therapies and prophylaxes against Escherichia coli infections such as urinary-tract infections. To construct these inhibitors, the α-d-mannopyranoside of high-mannose N-glycans, recognized with exclusive specificity on glycoprotein receptors by FimH, forms the basal structure. A hydrophobic aglycon is then linked to the mannose by the O1 oxygen inherently present in the α-anomeric configuration...
May 1, 2016: IUCrJ
Quan Hao
Nass et al. [IUCrJ (2016), 3, 180-191] have demonstrated that serial femtosecond crystallography (SFX) data collected at X-ray free-electron lasers (XFELs) can be successfully phased using only the weak anomalous scattering from the native S atoms.
May 1, 2016: IUCrJ
Geetha Bolla, Ashwini Nangia
A novel design strategy for cocrystals of a sulfonamide drug with pyridine carboxamides and cyclic amides is developed based on synthon identification as well as size and shape match of coformers. Binary adducts of acetazolamide (ACZ) with lactams (valerolactam and caprolactam, VLM, CPR), cyclic amides (2-pyridone, labeled as 2HP and its derivatives MeHP, OMeHP) and pyridine amides (nicotinamide and picolinamide, NAM, PAM) were obtained by manual grinding, and their single crystals by solution crystallization...
March 1, 2016: IUCrJ
Manabu Hoshino, Anupam Khutia, Hongzhu Xing, Yasuhide Inokuma, Makoto Fujita
Crystalline sponges are porous metal complexes that can absorb and orient common organic molecules in their pores and make them observable by conventional X-ray structure analysis (crystalline sponge method). In this study, all of the steps in the crystalline sponge method, including sponge crystal preparation, pore-solvent exchange, guest soaking, data collection and crystallographic analysis, are carefully examined and thoroughly optimized to provide reliable and meaningful chemical information as chemical crystallography...
March 1, 2016: IUCrJ
Ruben A Dilanian, Sophie R Williams, Andrew V Martin, Victor A Streltsov, Harry M Quiney
Serial femtosecond X-ray crystallography (SFX) has created new opportunities in the field of structural analysis of protein nanocrystals. The intensity and timescale characteristics of the X-ray free-electron laser sources used in SFX experiments necessitate the analysis of a large collection of individual crystals of variable shape and quality to ultimately solve a single, average crystal structure. Ensembles of crystals are commonly encountered in powder diffraction, but serial crystallography is different because each crystal is measured individually and can be oriented via indexing and merged into a three-dimensional data set, as is done for conventional crystallography data...
March 1, 2016: IUCrJ
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