An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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A short history of SHELX

A new approach that integrates data collection, data reduction, phasing and model building significantly accelerates the process of structure determination and on average minimizes the number of data sets and synchrotron time required for structure solution. Initial testing of the HKL-3000 system (the beta version was named HKL-2000_ph) with more than 140 novel structure determinations has proven its high value for MAD/SAD experiments. The heuristics for choosing the best computational strategy at different data resolution limits of phasing signal and crystal diffraction are being optimized. The typical end result is an interpretable electron-density map with a partially built structure and, in some cases, an almost complete refined model. The current development is oriented towards very fast structure solution in order to provide feedback during the diffraction experiment. Work is also proceeding towards improving the quality of phasing calculation and model building.

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HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.

Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.

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Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 A resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

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From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.

Pentameric ligand-gated ion channels (pLGICs) are key players in the early events of electrical signal transduction at chemical synapses. The family codes for a structurally conserved scaffold of channel proteins that open in response to the binding of neurotransmitter molecules. All proteins share a pentameric organization of identical or related subunits that consist of an extracellular ligand-binding domain followed by a transmembrane channel domain. The nicotinic acetylcholine receptor (nAChR) is the most thoroughly studied member of the pLGIC family (for recent reviews see refs 1-3). Two sources of structural information provided an architectural framework for the family. The structure of the soluble acetylcholine-binding protein (AChBP) defined the organization of the extracellular domain and revealed the chemical basis of ligand interaction. Electron microscopy studies of the nAChR from Torpedo electric ray have yielded a picture of the full-length protein and have recently led to the interpretation of an electron density map at 4.0 A resolution. Despite the wealth of experimental information, high-resolution structures of any family member have so far not been available. Until recently, the pLGICs were believed to be only expressed in multicellular eukaryotic organisms. The abundance of prokaryotic genome sequences, however, allowed the identification of several homologous proteins in bacterial sources. Here we present the X-ray structure of a prokaryotic pLGIC from the bacterium Erwinia chrysanthemi (ELIC) at 3.3 A resolution. Our study reveals the first structure of a pLGIC at high resolution and provides an important model system for the investigation of the general mechanisms of ion permeation and gating within the family.

X-ray structure of a prokaryotic pentameric ligand-gated ion channel

One approach to phasing of macromolecular crystal structure is to exploit the small changes in diffracted intensities induced by the inclusion of heavy atoms, to alter the wavelength in the presence of anomalous scatterers, or to use a combination thereof. In the SHELX suite of crystallographic programs, the computations involved in the respective phasing procedures are divided into three steps: (i) extraction of structure factors representing the substructure of heavy atoms and/or anomalous scatterers only (SHELXC; Sheldrick, 2004), (ii) determination of the substructure (SHELXD; Schneider & Sheldrick, 2002), (iii) calculation of initial phases based on the knowledge of the substructure and improvement of these phases by density modi®cation (SHELXE; Sheldrick, 2002). A number of crystal structures have been solved using the combination of the programs mentioned above. However, in particular for the inexperienced user, the creation of correct input ®les and the interpretation of the intermediate results can be a major obstacle.

HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs

Facile Syntheses of Selenium- and Tellurium-Containing Metal Cubanes, [Cp*M(.mu.3-E)]4 (Cp* = C5Me5; M = Rh, Ir, Ga; E = Se, Te), and X-ray Crystal Structures of (Cp*RhSe)4, (Cp*IrSe)4, (Cp*RhTe)4, (Cp*IrTe)4, and (Cp*GaTe)4

The Ecballium elaterium trypsin inhibitor II (EETI-II) belongs to the family of squash inhibitors and is one of the strongest inhibitors known for trypsin. The eight independent molecules of EETI-II in the crystal structure reported here provide a good opportunity to test the hypothesis that this small cystine-knot protein (knottin) is sufficiently rigid to be used as a molecular scaffold for protein-engineering purposes. To extend this test, the structures of two complexes of EETI-II with trypsin have also been determined, one carrying a four-amino-acid mutation of EETI-II. The remarkable similarity of these structures confirms the rigidity of the molecular framework and hence its suitability as a molecular scaffold.

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Structure of Ecballium Elaterium Trypsin Inhibitor II (Eeti-II): A Rigid Molecular Scaffold

Synthesis of (RSn)4X6 Adamantanes (X = O, S, Se) in Liquid Ammonia and in the Two-Phase System Liquid Ammonia/THF

A new pentamethylcyclopentadienyl titanoxane fluoride (C5Me5)4Ti4O5F2 (1b) has been synthesized from (C5Me5)4Ti4O5Cl2 using the fluorinating reagent Me3SnF. The fluorination of organotitanoxane chlorides proceeds via a proposed intermediate similar to the four-membered ring Ti(μ-Cl)(μ-F)Sn and the bridged Ti(μ-F)ClSnMe3 species. The reactions of 1b and [C5Me5Ti(μ-O)F]4 with AlR3 (R = Me, Et, CH2Ph) afforded the thermally unstable adducts [C5Me5Ti(μ-O)]4F4-n[(μ-F)AlR3]n (n = 1−4), which proceed with selective exchange of fluorine atoms for alkyl groups to give an eight-membered alkylated ring compound [C5Me5Ti(μ-O)R]4. The reactions of 1b and [C5Me5Ti(μ-O)F]4 with Me3SiCl result in exchange of fluorine for chlorine atoms. Moreover, using an excess of Me3SiCl leads to a novel oxygen−chlorine exchange reaction to give C5Me5TiCl3. The crystal structures of complexes (C5Me5)4Ti4O5X2 (X = Cl (1a), F (1b)), [C5Me5Ti(μ-O)]4F[(μ-F)AlMe3]3 (2b), [C5Me5Ti(μ-O)]4F3[(μ-F)Al(CH2Ph)3] (3a), and [C5Me5Ti(μ-O)Et]4 (4) hav...

Reactions of Organotitanoxane Fluorides with AlR3 (R = Me, Et, CH2Ph) and Me3SiCl: X-ray Crystal Structures of [C5Me5Ti(μ-O)]4F[(μ-F)AlMe3]3, [C5Me5Ti(μ-O)]4F3[(μ-F)Al(CH2Ph)3], [C5Me5Ti(μ-O)Et]4, and (C5Me5)4Ti4O5X2 (X = Cl and F)†

Thomas Pape

Papers

HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs

Facile Syntheses of Selenium- and Tellurium-Containing Metal Cubanes, [CpM(.mu.3-E)]4 (Cp = C5Me5; M = Rh, Ir, Ga; E = Se, Te), and X-ray Crystal Structures of (CpRhSe)4, (CpIrSe)4, (CpRhTe)4, (CpIrTe)4, and (Cp*GaTe)4

Structure of Ecballium Elaterium Trypsin Inhibitor II (Eeti-II): A Rigid Molecular Scaffold

Synthesis of (RSn)4X6 Adamantanes (X = O, S, Se) in Liquid Ammonia and in the Two-Phase System Liquid Ammonia/THF

Reactions of Organotitanoxane Fluorides with AlR3 (R = Me, Et, CH2Ph) and Me3SiCl: X-ray Crystal Structures of [C5Me5Ti(μ-O)]4F[(μ-F)AlMe3]3, [C5Me5Ti(μ-O)]4F3[(μ-F)Al(CH2Ph)3], [C5Me5Ti(μ-O)Et]4, and (C5Me5)4Ti4O5X2 (X = Cl and F)†