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Acta Cryst. (2013). A69, 140-150 [ doi:10.1107/S0108767312047150 ] Structural constraints on the three-dimensional geometry of simple viruses: case studies of a new predictive toolT. Keef, J. P. Wardman, N. A. Ranson, P. G. Stockley and R. TwarockActa Cryst. (2013). A69, 151-163 [ doi:10.1107/S0108767312047162 ] From an affine extended icosahedral group towards a toolkit for viral architectureA. JannerThe exterior surfaces of icosahedral viruses are classified according to the T-numbers of Caspar and Klug, akin to crystal growth forms in crystallography. In analogy to the characterization of internal atomic structures of crystal growth forms via space groups, the interior organization of viruses is investigated here using icosahedral affine extensions by appropriate (indexed) translations. The analysis reveals a previously unrecognized structural interdependence of the shapes and sizes of different viral components, providing novel insights into structural constraints on virus architecture. | ![]() Model prediction correlates well with the three-dimensional structure of hepatitis B virus. | |
Acta Cryst. (2013). B69, 1-16 [ doi:10.1107/S2052519212051366 ] The charge-flipping algorithm in crystallographyL. PalatinusDual-space iterative algorithms are conceptually simple, yet very efficient phasing algorithms applicable for solution of the crystallographic phase problem. Among the broad family of these algorithms the charge flipping algorithm (CFA) is the most widely used algorithm in crystallography. The article reviews the history of the dual-space algorithms in crystallography, the relationship of CFA to other dual-space algorithms, the variants of CFA, and the applications of CFA to routine structure solution, solution of aperiodic structures, powder diffraction data, macromolecular crystallography and single-particle imaging. | ![]() Iteration paths of several dual-space algorithms for a convex consistent problem (upper panel) and non-convex inconsistent problem (lower panel). ER = error reduction, CF = charge flipping, DM = difference map, AAR = averaged alternating reflections, RAAR = relaxed averaged alternating reflections. | |
Acta Cryst. (2013). C69, 285-288 [ doi:10.1107/S0108270113003806 ] Solid-state tautomeric structure and invariom refinement of a novel and potent HIV integrase inhibitorJ. Bacsa, M. Okello, P. Singh and V. NairFormula: C27H22F3N3O5 HIV-1 integrase catalyzes the integration of viral DNA into human chromosomal DNA, which is the “point of no return” in an HIV infection. The conformation and tautomeric structure of a potent and novel integrase inhibitor with potential for HIV/AIDS therapeutics has been resolved. The electron-density distribution derived from invariom model scattering factors was a faithful mapping of the electron density in the crystal. The electrostatic potential of this molecule derived from the electron density could provide information on this molecule's ability to inhibit the activity of the integrase. | ![]() | |
Acta Cryst. (2013). D69, 150-167 [ doi:10.1107/S0907444912044423 ] Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structuresE. Pozharski, C. X. Weichenberger and B. RuppDetermining protein structures in complex with a small-molecule ligand is essential to the understanding of biologically important molecular interactions and in drug design. Electron density is the primary evidence which supports a particular ligand-binding mode in a corresponding complex structure. Inspection of deposited structure models reveals low real-space correlation coefficients for a large number of small-molecule ligands. Several classes of detected problems are analyzed, and suggestions for improvement in training of crystallographers and model validation are provided. | ![]() Missing density: extended glycosylations. The specific conformation of the last three -D-mannose moieties (A5–A7) of the extended branched glycosylation in PDB entry 3ib0 [Mir et al. (2009). Biophys. J. 97, 3178–3186] is unsupported by electron density in the structure of bovine lactotransferrin, while the first two sugar moieties (A3–A4) are clearly present. The 1.4 Å resolution mFo – DFc map contoured at +3 (green) was calculated after refining a model omitting the sugar moieties of the glycosylation site. | |
Acta Cryst. (2013). E69, o217 [ doi:10.1107/S1600536813000305 ] meso-4,4'-Difluoro-2,2'-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl]bis(methylene)}diphenolA. Rivera, D. Quiroga, J. Ríos-Motta, M. Kuceraková and M. DusekIn 1,1-diamines the conformations are strongly disfavored if the unshared electron pairs on nonadjacent N atoms are parallel or syn-axial. The consequences are seen in the preferred conformation of certain heterocyclic rings. Eliel proposed to call this phenomenon the “rabbit-ear effect”. The crystal structure of the title compound established the existence of a “rabbit-ear effect” in the N–C–N aminal motif in which the lone pairs of the N atoms are located in syn disposition. The title compound is a good model to study intracyclic stereoelectronic effects. | ![]() A perspective view of the title compound, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii. Hydrogen bonds are drawn as dashed lines. | |
Acta Cryst. (2013). F69, 25-34 [ doi:10.1107/S1744309112044739 ] The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discoveryL. Moynie, R. Schnell, S. A. McMahon, T. Sandalova, W. A. Boulkerou, J. W. Schmidberger, M. Alphey, C. Cukier, F. Duthie, J. Kopec, H. Liu, A. Jacewicz, W. N. Hunter, J. H. Naismith and G. SchneiderBacteria, particularly Gram-negative species, present a serious challenge to human health. At worst, increasingly antibiotic-resistant pathogens threaten to undo over half a century of medical progress. Traditionally, antibiotics were discovered empirically through large screening efforts of natural products. The power of modern structural biology allows antibiotic discovery to start with atomic resolution information of potential drug targets. Here, we report a suite of protein crystal structures from the pathogen Pseudomonas aeruginosa that provide rational starting points for future antibiotic discovery. | ![]() Crystal structure of HemD from the pathogen Pseudomonas aeruginosa. The enzyme is located at a metabolic branching point leading to the biosynthesis of haem, sirohaem or vitamin B12. | |
J. Appl. Cryst. (2013). 46, 262-266 [ doi:10.1107/S0021889812042781 ] An X-ray diffractometer coupled with diffuse reflectance infrared Fourier transform spectroscopy and gas chromatography for in situ and in operando characterization: an innovative analytical laboratory instrumentL. Braconnier, I. Clémençon, C. Legens, V. Moizan, F. Diehl, H. Pillière, P. Echegut, D. De Sousa Meneses and Y. SchuurmanFor the first time, an innovative reaction cell allowing simultaneous XRD and DRIFT spectroscopy characterizations has been developed for in situ and in operando applications at a laboratory scale. Thanks to the high temperatures (873 K) and high pressures (18 bar) supported, this tool, associated with an online gas chromatograph, is well adapted to heterogeneous catalysis as chemical reactions take place at the surface of the material and can be influenced by its structure. | ![]() | |
J. Synchrotron Rad. (2013). 20, 355-365 [ doi:10.1107/S090904951204856X ] X-ray diffraction imaging of metal-oxide epitaxial tunnel junctions made by optical lithography: use of focused and unfocused X-ray beamsC. Mocuta, A. Barbier, S. Stanescu, S. Matzen, J.-B. Moussy and E. ZieglerMetal–oxide magnetic tunnel junctions, consisting of an insulating layer sandwiched between two electrodes made of hard and soft ferromagnetic layered materials, are highly sensitive sensors for spintronic applications. Typical sizes in the micrometre range favored investigations using X-ray imaging techniques. The layers, differing either by their lattice parameter or by crystalline structure, were easily distinguishable from each other by X-ray diffraction contrast, while raster imaging and local probe diffraction allowed defects and distortions at both the macro- and the microscale to be detected and localized. | ![]() Schematics of the X-ray diffraction imaging experiment and the model sample used (epitaxial magnetic tunnel junction). | |





-1,6/
-1,4-specific glucansucrase GTFA from Lactobacillus reuteri 121. Acta Cryst. F68, 1448-1454. 
















5-dioxaphospholan-2-yloxy)butan-2-olato-
2O,P]oxido(triphenylphosphane-
P)rhenium(V). Acta Cryst. E68, m605-m606. 
















S;
2S:S'-(triphenylphosphane-
P)palladium(II). Acta Cryst. E67, m1518. 















-form of chlorpropamide on cooling to 100 K. Acta Cryst. B67, 163-176. 













,7
,12
-tris(4-nitrobenzoyloxy)-5
-cholan-24-yl] disulfide-ethyl acetate-n-hexane (4/4/1). Acta Cryst. E67, o74-o75. 









2-6,6'-Dimethoxy-2,2'-[butane-1,4-diylbis(nitrilomethylidyne)]diphenolato}trinitratocopper(II)neodymium(III). Acta Cryst. E66, m1423. 















-SrB4O7. Acta Cryst. E66, i48. 







-D-erythrofuranosyl)thymine. Acta Cryst. E66, o404. 







-spirostan-3
-yl acetate. Acta Cryst. E65, o2954-o2955. 




-phosphoglucomutase (TM1254) from Thermotoga maritima. Acta Cryst. F65, 1218-1221. 












-lactamase (AmpCD) from an Escherichia coli clinical isolate with a tripeptide deletion (Gly286-Ser287-Asp288) in the H10 helix. Acta Cryst. F65, 540-543. 




3-allyl)4Cl2(OH)2(CO)8: the first cubane-type Mo2+ organometallic complex with
3-OH and
3-Cl bridges. Acta Cryst. C65, m168-m170. 

5-pentamethylcyclopentadienyl)cobalt(II). Acta Cryst. E65, m391. 















4N,N',N'',N'''}bis(trifluoromethanesulfanato-
O)copper(II). Acta Cryst. E64, m1435. 












-2 polymorphs of trans-mono-unsaturated triacylglycerols and related fully saturated triacylglycerols. Acta Cryst. B64, 240-248. 
'-2 polymorphs of trans-mono-unsaturated triacylglycerols and related saturated TAGs and their polymorphic stability. Acta Cryst. B64, 249-259. 









2-hydroxido-bis[dioxouranium(VI)]]-di-
2-2-pyridylacetato-
3O,N:O';
3O:O',N]. Acta Cryst. C64, m50-m52. 















3-1,1-dioxo-1,2-benzoisothiazole-3-thiolato-
3N:S3:S3)silver(I)]. Acta Cryst. C63, m395-m397. 

































2S,S')bismuth(III). Acta Cryst. E62, m2552-m2554. 






5-hydrogenphosphato-pentamolybdate(VI) tetrahydrate. Acta Cryst. C62, m355-m357. 





-GaPO4. Acta Cryst. A62, 1-10. 

















-tetraethoxyborato]. Acta Cryst. C61, m417-m418. 










5-cyclopentadienyl)tungstenio]indium. Acta Cryst. E61, m945-m946. 





-acetato-acetonitriletris(
-N,N'-diphenylformamidinato)diruthenium tetrafluoroborate dichloromethane hemisolvate. Acta Cryst. C61, m71-m73. 















-chloro-bis[dichloropalladium(II)]. Acta Cryst. C60, m426-m430. 

-Diphenylphosphido-
-hydrido-bis[carbonyl(
5-cyclopentadienyl)iron(II)]. Acta Cryst. E60, m1284-m1285. 









-ray and neutron diffraction studies of CoF2: magnetostriction, electron density and magnetic moments. Acta Cryst. A60, 51-57. 


Arg surface mutations on the crystallization of the globular domain of RhoGDI. Acta Cryst. D60, 275-280. 



-AlCrFe phase by electron crystallography. Acta Cryst. A59, 526-539. 




























O)zinc(II). Acta Cryst. C59, m18-m20. 

-
-Stacking and nitro-
-stacking interactions of 1-(4-nitrophenyl)-4-phenyl-2,4-bis(phenylethynyl)butadiene. Acta Cryst. E59, o227-o229. 


-sheet structure formed by C-H
O hydrogen bonds between the thiazole rings and amide bonds of a dimeric desoxazoline ascidiacyclamide analogue. Acta Cryst. E57, o834-o838. 









C-terminal SH2-peptide complex. Acta Cryst. D57, 1397-1404. 





O hydrogen bond in urea-phosphoric acid (1/1). Acta Cryst. B57, 435-439. 



















-galactose and N-acetyllactosamine and a comparative study of carbohydrate binding in Gal/GalNAc-specific legume lectins. Acta Cryst. D55, 1375-1382. 











-oxo-bis[bis(bipyridine-N,N')manganese(III, IV)] Triperchlorate Bis(nitrobenzene) Hemihydrate. Acta Cryst. C54, 1797-1799. 






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