The preferred orientation growth characteristics and surface roughness of polycrystalline bis­muth (Bi) thin films fabricated on glass substrates using the molecular beam epitaxy method were investigated at temperatures ranging from 18 to 150°C. The crystallization and morphology were analyzed in detail and the polycrystalline metal film structure-zone model (SZM) was modified to fit the polycrystalline Bi thin film. The boundary temperature between Zone T and Zone II in the SZM shifted to higher temperatures with the increase in film thickness or the decrease of growth rate. Furthermore, the effect of the thickness and surface roughness on the transport properties was investigated, especially for Bi thin films in Zone II. A two-transport channels model was adopted to reveal the influence of the film thickness on the competition between the metallic surface states and the semiconducting bulk states, which is consistent with the results of Bi single-crystal films. Therefore, the polycrystalline Bi thin films are expected to replace the single-crystal films in the application of spintronic devices.

Using the typical WC–Co cemented carbide as an example, the interactions of dislocations within the ceramic matrix and the binder metal, as well as the possible cooperation and competition between the matrix and binder during deformation of the nanocrystalline cermets, were studied by molecular dynamics simulations. It was found that at the same level of strain, the dislocations in Co have more complex configurations in the cermet with higher Co content. With loading, the ratio between mobile and sessile dislocations in Co becomes stable earlier in the high-Co cermet. The strain threshold for the nucleation of dislocations in WC increases with Co content. At the later stage of deformation, the growth rate of WC dislocation density increases more rapidly in the cermet with lower Co content, which exhibits an opposite tendency compared with Co dislocation density. The relative contribution of Co and WC to the plasticity of the cermet varies in the deformation process. With a low Co content, the density of WC dislocations becomes higher than that of Co dislocations at larger strains, indicating that WC may contribute more than Co to the plasticity of the nanocrystalline cermet at the final deformation stage. The findings in the present work will be applicable to a large variety of ceramic–metal composite materials.

A series of Co2−xRuxMnSi (x = 0, 0.25, 0.5, 0.75, 1) Heusler compounds were successfully synthesized. The heat-treatment conditions were crucial to make the materials form a single phase with a Heusler structure. With increasing Ru content, the half-metallic gap, lattice parameters and magnetization are continuously adjustable in a wide range. The Co2−xRuxMnSi (x = 0, 0.25) compounds are rigorous half-metals and show a T3 dependence of resistance at low temperature. The Co2−xRuxMnSi (x = 0.5, 0.75, 1) Heusler compounds are the nearly half-metallic materials and show a semiconductive dependence of resistance at low temperature. The experimental magnetization is consistent with that in theory and follows the Slater–Pauling rule. The Curie temperature is higher than 750 K for all Co2−xRuxMnSi Heusler compounds.

Several pathogenic bacteria utilize sialic acid, including host-derived N-acetylneuraminic acid (Neu5Ac), in at least two ways: they use it as a nutrient source and as a host-evasion strategy by coating themselves with Neu5Ac. Given the significant role of sialic acid in pathogenesis and host-gut colonization by various pathogenic bacteria, including Neisseria meningitidis, Haemophilus influenzae, Pasteurella multocida and Vibrio cholerae, several enzymes of the sialic acid catabolic, biosynthetic and incorporation pathways are considered to be potential drug targets. In this work, findings on the structural and functional characterization of CMP-N-acetylneuraminate synthetase (CMAS), a key enzyme in the incorporation pathway, from Vibrio cholerae are reported. CMAS catalyzes the synthesis of CMP-sialic acid by utilizing CTP and sialic acid. Crystal structures of the apo and the CDP-bound forms of the enzyme were determined, which allowed the identification of the metal cofactor Mg2+ in the active site interacting with CDP and the invariant Asp215 residue. While open and closed structural forms of the enzyme from eukaryotic and other bacterial species have already been characterized, a partially closed structure of V. cholerae CMAS (VcCMAS) observed upon CDP binding, representing an intermediate state, is reported here. The kinetic data suggest that VcCMAS is capable of activating the two most common sialic acid derivatives, Neu5Ac and Neu5Gc. Amino-acid sequence and structural comparison of the active site of VcCMAS with those of eukaryotic and other bacterial counterparts reveal a diverse hydrophobic pocket that interacts with the C5 substituents of sialic acid. Analyses of the thermodynamic signatures obtained from the binding of the nucleotide (CTP) and the product (CMP-sialic acid) to VcCMAS provide fundamental information on the energetics of the binding process.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10−4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10−3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.

The laser annealing process for AuNi nanoparticles has been visualized using coherent X-ray diffraction imaging (CXDI). AuNi bimetallic alloy nanoparticles, originally phase separated due to the miscibility gap, transform to metastable mixed alloy particles with rounded surface as they are irradiated by laser pulses. A three-dimensional CXDI shows that the internal part of the AuNi particles is in the mixed phase with preferred compositions at ∼29 at% of Au and ∼90 at% of Au.

The composition of occupied and unoccupied electronic states in the vicinity of Fermi energies is vital for all materials and relates to their physical, chemical and mechanical properties. This work demonstrates how the combination of resonant and non-resonant X-ray emission spectroscopies supplemented with theoretical modelling allows for quantitative analysis of electronic states in 5d transition metal and metal-oxide materials. Application of X-rays provides element selectivity that, in combination with the penetrating properties of hard X-rays, allows determination of the composition of electronic states under working conditions, i.e. non-vacuum environment. Tungsten metal and tungsten oxide are evaluated to show the capability to simultaneously assess composition of around-band-gap electronic states as well as the character and magnitude of the crystal field splitting.

An error in the article by Gao, Zhang, Zhu, Wu, Mo, Pan, Liu & Jiang [J. Appl. Cryst. (2019), 52, 637–642] is corrected.

Single-crystalline-like thin films composed of crystallographically aligned grains are a new prototype of 2D materials developed recently for low-cost and high-performance flexible electronics as well as second-generation high-temperature superconductors. In this work, significant texture improvement in single-crystalline-like materials is achieved through growth of a 330 nm-thick silver layer.

A new ZnII metallocryptand is presented, with an unprecedented diflexure helix.

The title compound, C11H11NO5, has a nearly planar geometry. In the crystal, the molecules are assembled into chains parallel to the [overline{1}11] direction by O—H...O and C—H...O hydrogen bonds.

Today the Smithsonian Institution announced Eva J. Pell, Senior Vice President for Research and Dean of the Graduate School at Pennsylvania State University, will be the new Under Secretary for Science at the Institution.

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In a new paper, Harvard-Smithsonian Center for Astrophysics astronomer Hagai Perets studies the role of binary planetesimals--clumps that orbit each other and jointly mature via three basic processes.

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A. sediba was discovered in 2008 in the Malapa Cave at the Cradle of Humankind World Heritage Site located outside Johannesburg.

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The predictability and scale of seasonal changes in a habitat help determine the distance migratory species move and whether the animals always travel together to the same place or independently to different locations.

The post Changes in vegetation determine how animals migrate, scientists find in new National Zoo study appeared first on Smithsonian Insider.

Five cheetah cubs were born May 28 to 6-year-old Amani at the Smithsonian Conservation Biology Institute in Front Royal, Va. Amani is a dedicated mother according to keepers, who have observed her nursing and grooming the cubs.

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Researchers at the Smithsonian Conservation Biology Institute have discovered why older females are rarely able to reproduce—and hope to use this information to introduce vital […]

The post New finding may enable scientists to bolster genetic diversity of captive cheetah population appeared first on Smithsonian Insider.

A fragment of whale rib found in a North Carolina strip mine is offering scientists a rare glimpse at the interactions between prehistoric sharks and whales some 3- to 4- million years ago during the Pliocene.

The post Details of ancient shark attack preserved in fossil whale bone appeared first on Smithsonian Insider.

Astronomers are confident the Cygnus X-1 system contains a black hole, and with these latest studies they have remarkably precise values of its mass, spin, and distance from Earth.

The post New details on birth of black hole Cygnus X-1 revealed by Chandra X-ray Observatory appeared first on Smithsonian Insider.

Imagine a gas giant planet spanning three times more sky than the Moon looming over the molten landscape of a lava world. This alien vista exists in the newly discovered two-planet system of Kepler-36.

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The discovery of the first transiting circumbinary multi-planet system: two planets orbiting around a pair of stars, is announced by astronomers.

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Clearly visible connecting the dark-purple cephalopods was the white “terminal organ” or penis of the male, extending out through the male’s funnel.

The post First detailed sex video of deep-sea squid resolves long-standing mysteries as to how these animals mate appeared first on Smithsonian Insider.

To download the free e-book Best of Both Worlds: Museums, Libraries, and Archives in a Digital Age, by G. Wayne Clough, Secretary of the Smithsonian, […]

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Recently crowned the “astronomy photo of the year” by Slate’s Bad Astronomy blog, a new image of a region of Orion’s belt reveals the deepest […]

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The planet’s last stronghold of wild cheetahs (Acinonyx jubatus) is losing genetic diversity at an alarming rate according to a new study from the Smithsonian […]

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A new study from the Smithsonian Conservation Biology Institute (SCBI) is helping make headway in an area of animal management that has historically proven challenging: […]

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Olivia R. Grafinger, Genya Gorshtein, Tyler Stirling, Megan I. Brasher, and Marc G. Coppolino

Malignant cancer cells can invade extracellular matrix (ECM) through the formation of F-actin-rich subcellular structures termed invadopodia. ECM degradation at invadopodia is mediated by matrix metalloproteinases (MMPs), and recent findings indicate that membrane-anchored membrane type 1-matrix metalloproteinase (MT1-MMP) has a primary role in this process. Maintenance of an invasive phenotype is dependent on internalization of MT1-MMP from the plasma membrane and its recycling to sites of ECM remodeling. Internalization of MT1-MMP is dependent on its phosphorylation, and here we examine the role of β1 integrin-mediated signaling in this process. Activation of β1 integrin using the antibody P4G11 induced phosphorylation and internalization of MT1-MMP and resulted in increased cellular invasiveness and invadopodium formation in vitro. We also observed phosphorylation of Src and epidermal growth factor receptor (EGFR) and an increase in their association in response to β1 integrin activation, and determined that Src and EGFR promote phosphorylation of MT1-MMP on Thr⁵⁶⁷. These results suggest that MT1-MMP phosphorylation is regulated by a β1 integrin-Src-EGFR signaling pathway that promotes recycling of MT1-MMP to sites of invadopodia formation during cancer cell invasion.

Karolina Losenkova, Mariachiara Zuccarini, Marika Karikoski, Juha Laurila, Detlev Boison, Sirpa Jalkanen, and Gennady G. Yegutkin

Extracellular adenosine mediates diverse anti-inflammatory, angiogenic and vasoactive effects and becomes an important therapeutic target for cancer, which has been translated into clinical trials. This study was designed to comprehensively assess adenosine metabolism in prostate and breast cancer cells. We identified cellular adenosine turnover as a complex cascade, comprised of (a) the ectoenzymatic breakdown of ATP via sequential nucleotide pyrophosphatase/phosphodiesterase-1, ecto-5’-nucleotidase/CD73 and adenosine deaminase reactions, and ATP re-synthesis through counteracting adenylate kinase and nucleoside diphosphokinase; (b) the uptake of nucleotide-derived adenosine via equilibrative nucleoside transporters; and (c) the intracellular adenosine phosphorylation into ATP by adenosine kinase and other nucleotide kinases. The exposure of cancer cells to 1% O₂ for 24 hours triggered ~2-fold up-regulation of CD73, without affecting nucleoside transporters, adenosine kinase activity and cellular ATP content. The ability of adenosine to inhibit the tumor-initiating potential of breast cancer cells via receptor-independent mechanism was confirmed in vivo using a xenograft mouse model. The existence of redundant pathways controlling extracellular and intracellular adenosine provides a sufficient justification for reexamination of the current concepts of cellular purine homeostasis and signaling in cancer.

Ganlu Deng, Yihong Chen, Cao Guo, Ling Yin, Ying Han, Yiyi Li, Yaojie Fu, Changjing Cai, Hong Shen, and Shan Zeng

Epithelial-mesenchymal transition (EMT) is a crucial process for cancer cells to acquire metastatic potential, which primarily causes death in gastric cancer (GC) patients. Bone morphogenetic protein 4 (BMP4) is a member of the TGF-β family that plays an indispensable role in human cancers. However, little is known about its roles in GC metastasis. In this study, BMP4 was found to be frequently overexpressed in GC tissues and was correlated with patient's poor prognosis. BMP4 was upregulated in GC cell lines and promoted EMT and metastasis of GC cells both in vitro and in vivo, while knockdown of BMP4 significantly inhibited EMT and metastasis of GC cells. Meanwhile, the inhibitor of DNA binding 1 (Id1) was identified as a downstream target of BMP4 by PCR arrays and upregulated via Smad1/5/8 phosphorylation. Id1 knockdown attenuated BMP4-induced EMT and invasion in GC cells. Moreover, Id1 overexpression in BMP4 knockdown cells restored the promotion of EMT and cell invasion. In summary, BMP4 induced EMT to promote GC metastasis by upregulating Id1 expression. Antagonizing BMP4 may be a potential therapeutic strategy in GC metastasis.

The number and diversity of tectonic landforms in our solar system “is truly remarkable,” Watters and Schultz write. Photographs of these structures have stimulated a range of scholarly investigations.

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A novel approach for finding and evaluating structural models of small metallic nanoparticles is presented. Rather than fitting a single model with many degrees of freedom, libraries of clusters from multiple structural motifs are built algorithmically and individually refined against experimental pair distribution functions. Each cluster fit is highly constrained. The approach, called cluster-mining, returns all candidate structure models that are consistent with the data as measured by a goodness of fit. It is highly automated, easy to use, and yields models that are more physically realistic and result in better agreement to the data than models based on cubic close-packed crystallographic cores, often reported in the literature for metallic nanoparticles.

Bruce Campbell, of the Center for Earth and Planetary Studies at the Smithsonian's National Air and Space Museum, is at the National Radio Astronomy Observatory in Green Bank, W. Va., to make a radar map of the Moon.

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The three male cheetahs that left the Zoo's D.C. campus in 2009 returned in November and are now on exhibit. The five-and-a-half-year-old brothers―Draco, Granger, and Zabini, named after characters in the Harry Potter stories―have been living at the Zoo's Smithsonian Conservation Biology Institute's Cheetah Science Facility in Front Royal, Virginia.

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The post Many years of research are celebrated in the December 2010 birth of two cheetah cubs at the Smithsonian Conservation Biology Institute appeared first on Smithsonian Insider.

Jim Zimbelman, planetary geologist in the Center for Earth and Planetary Studies at the Smithsonian’s National Air and Space Museum, shares his three favorite images from the exhibition "Beyond: Visions of Our Solar System.” On view at the Air and Space Museum through May 2, 2011, the exhibition by artist Michael Benson combines art, science, photography and exploration to unveil the diverse landscapes found on the planets in our Solar System.

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The post How do paleontologists identify dinosaur teeth? Smithsonian Curator Matthew Carrano identifies Cretaceous dinosaur teeth from the Washington D.C. area. appeared first on Smithsonian Insider.

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The post Samuel P. Langley, Secretary of the Smithsonian, and his development of the ill-fated Aerodrome A appeared first on Smithsonian Insider.

How do you train a wild animal to come back to you after you have set it free? If it is a fringe-lipped bat, Trachops […]

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The start of spring brought a cheetah cub boom to the Smithsonian Conservation Biology Institute (SCBI) in Front Royal, Va., where two large litters were […]

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It's late October, which means  more and more stores are decorating for Christmas. 

Steve Julian:  Business analyst Mark Lacter, whatever happened to "better late than never?" 

Mark Lacter: Steve, retailers never want to sell late because it often means having to reduce the price. They're looking to start out as soon as possible - these last three months represent their biggest payday of the year. And here in California people do seem to be buying stuff - consumer spending has been up for 14 consecutive quarters, going back to the spring of 2009, and taxable sales are up almost 5 percent from the peak levels before the recession. Another good sign is Chapman University's index of consumer sentiment, which is at its highest level since the beginning of the recession in late 2007. All these indicators explain why the state economy is generally outpacing the rest of the nation.

Julian: There has to be a "but" in here someplace…

 Lacter: The "but" is that only 60 percent of the jobs lost during the downturn have been recovered, and the unemployment rate in many parts of the state, including L.A. County, is still at or above 10 percent, which isn't what you'd call a healthy economy. And that's why holiday shopping this year could end up being sort of hit and miss. Folks who have well-paying jobs and a bunch of their money in the stock market - and Southern California has its share of both - those folks will probably be spending good amounts. 

Julian: Are there geographic tell-tale signs?

Lacter: The closer to the coast you go, the more spending there's likely to be. But it's a different story if you're feeling vulnerable about your job or in the amount of savings you have in the bank. So you have retailers once again coming up with ways of reaching as many budget-conscious folks as possible, as early as possible. The most obvious move is opening their stores on Thanksgiving night - Macy's is the latest of the chains to get a head start on Black Friday (Target, Kohl's, Walmart and J.C. Penney will also be open). Another strategy is matching your prices with the prices on Amazon and other online retailers - also, retailers will use mobile apps and arrange in-store pickup of online purchases. All told, expect holiday sales to run 3 percent ahead of last year, with the L.A. area likely to be a bit higher. Decent, but not great.

 Julian: What's the message to consumers now: buy or not buy?

 Lacter: Well, we'll start with the good news - gasoline prices are at their lowest level since the beginning of the year, with an average gallon of regular in the L.A. area running $3.75, according to the Auto Club. And barring any refinery fires or international catastrophes, the numbers might keep falling into November and December, which could incentivize consumers to buy a little more at the shopping malls. Here's some more good news - the L.A. area has seen a huge drop in the number of homeowners who are underwater, which happens when the value of a property is less than the amount that's owed on the property. This of course was a big problem during the recession, but over the last year the median home values have gone up between 20 percent and 30 percent. 

 Julian: And if your equity is positive instead of negative, you'll probably feel more confident about spending. 

 Lacter: That's right. But there are also deterrents to spending - as has been reported, a few hundred thousand Californians lose their individual health care policies by the end of the year because their plans don't meet the requirements of the Affordable Care Act. Policyholders will be stuck in many cases with a premium increase, possibly a big increase. Now it's possible that in the long run these folks will be better off with a more inclusive plan that results in lower out-of-pocket expenses. But it'a hard to ignore the sticker shock of having to shell out, say, $250 a month instead of $100.

 Julian: There goes the holiday list...

 Lacter: For those folks, yes. And even though L.A. consumers do a good job of separating their feelings about Washington with their desire to spend, the economy is bound to slow down a little. So Steve, just don't count on that $9,000 fur vest I was going to get you for Christmas. Sorry about that…

Mark Lacter writes for Los Angeles Magazine and pens the business blog at LA Observed.com.

This content is from Southern California Public Radio. View the original story at SCPR.org.

Recent analysis using DNA sequencing of ancient Roman pills found aboard a ship that sank in Italy’s Gulf of Baratti between 140 -120 B.C, has revealed that the medicines consist of material from simple garden plants, namely carrot, radish, parsley, celery, wild onion and cabbage.

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The discovery of starch granules in the calculus on Neandertal teeth provides direct evidence that they made sophisticated, thoughtful food choices and ate more nutrient-rich plants, for example date palms, legumes and grains such as barley.

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Is it foolish to be optimistic about our environment and its future prospects? Every day, we hear dire warnings about the health of the planet […]

The post The Argument for Environmental Optimism: Opinion by Smithsonian Secretary David J. Skorton appeared first on Smithsonian Insider.

No green thumb? You don’t need to water these dazzling orchids to enjoy them. More than 8,000 living specimens in the Smithsonian Gardens Orchid Collection […]

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This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection of tips and tricks on recognizing and handling aspects of data collection, structure modelling and refinement, and the interpretation of results.

In small-molecule single-crystal structure determination, we now have at our disposal an inspiring range of fantastic diffractometers with better, brighter sources, and faster, more sensitive detectors. Faster and more powerful computers provide integrated tools and software with impressive graphical user interfaces. Yet these tools can lead to the temptation not to check the work thoroughly and one can too easily overlook tell-tale signs that something might be amiss in a structure determination; validation with checkCIF is not always revealing. This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection tips and tricks on recognizing and handling aspects that one should constantly be aware of. Topics include a pitfall when setting up data collections, the usefulness of reciprocal lattice layer images, processing twinned data, tips for disorder modelling and the use of restraints, ensuring hydrogen atoms are added to a model correctly, validation beyond checkCIF, and the derivation and interpretation of the final results.