Refinement of macromolecular structures against neutron data with SHELXL2013

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis

The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.

Towards inhibitors of glycosyltransferases: A novel approach to the synthesis of 3-acetamido-3-deoxy-D-psicofuranose derivatives

A novel synthetic strategy leading to 3-acetamido-3-deoxy-D-psicofuranose 9 is presented. The latter compound, after some manipulations, was transformed into fully protected 3-acetamido-3-deoxy-D-psicofuranose 11 as a potential substrate for the synthesis of N-acetylglucosaminyltransferase inhibitors designed by computational methods. After the attempted thioglycosylation of 11 with EtSH in the presence of BF3·OEt2, 2-methyloxazoline derivatives 13 and 14 were isolated.

The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source

The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. The instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. The instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.

New method to compute Rcomplete enables maximum likelihood refinement for small datasets

The crystallographic reliability index [Formula: see text] is based on a method proposed more than two decades ago. Because its calculation is computationally expensive its use did not spread into the crystallographic community in favor of the cross-validation method known as [Formula: see text]. The importance of [Formula: see text] has grown beyond a pure validation tool. However, its application requires a sufficiently large dataset. In this work we assess the reliability of [Formula: see text] and we compare it with k-fold cross-validation, bootstrapping, and jackknifing. As opposed to proper cross-validation as realized with [Formula: see text], [Formula: see text] relies on a method of reducing bias from the structural model. We compare two different methods reducing model bias and question the widely spread notion that random parameter shifts are required for this purpose. We show that [Formula: see text] has as little statistical bias as [Formula: see text] with the benefit of a much smaller variance. Because the calculation of [Formula: see text] is based on the entire dataset instead of a small subset, it allows the estimation of maximum likelihood parameters even for small datasets. [Formula: see text] enables maximum likelihood-based refinement to be extended to virtually all areas of crystallographic structure determination including high-pressure studies, neutron diffraction studies, and datasets from free electron lasers.

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Synthesis and characterization of a disordered variant of KB5O7(OH)2

The potassium pentaborate KB5O7(OH)2 reported herein crystallizes in the monoclinic space group P21 /c (no. 14) with the lattice parameters a = 904.8(2), b = 753.2(2), c = 1214.9(5) pm, β = 117.16(2)°, and V = 0.73663(5) nm3 (Z = 4). It is a disordered structural variant of an already known compound with the same composition (a = 766.90(3), b = 904.45(3), c = 1223.04(4) pm, β = 119.132(2)°, and V = 0.74101(5) nm3 (Z = 4)) reported by Wu in 2011. The disorder of the potassium cation in the single crystal structure determination of KB5O7(OH)2 presented here leads to a remarkably elongated a axis and a corresponding reduction of the length of the b axis in comparison to the ordered compound. The disordered variant was obtained through a hydrothermal synthesis from KNO3, B2O3, and Ce(NO3)3·6H2O with a molar ratio of 1:1:0.07.

Structure of magnesium selenate enneahydrate, MgSeO4·9H2O, from 5 to 250 K using neutron time-of-flight Laue diffraction

The complete structure of MgSeO4·9H2O has been refined from neutron single-crystal diffraction data obtained at 5, 100, 175 and 250 K. It is monoclinic, space group P2₁/c, Z = 4, with unit-cell parameters a = 7.222 (2), b = 10.484 (3), c = 17.327 (4) Å, β = 109.57 (2)°, and V = 1236.1 (6) Å(3) [ρ(calc) = 1770 (1) kg m(-3)] at 5 K. The structure consists of isolated [Mg(H2O)6](2+) octahedra, [SeO4](2-) tetrahedra and three interstitial lattice water molecules, all on sites of symmetry 1. The positions of the H atoms agree well with those inferred on the basis of geometrical considerations in the prior X-ray powder diffraction structure determination: no evidence of orientational disorder of the water molecules is apparent in the temperature range studied. Six of the nine water molecules are hydrogen bonded to one another to form a unique centrosymmetric dodecamer, (H2O)12. Raman spectra have been acquired in the range 170-4000 cm(-1) at 259 and 78 K; ab initio calculations, using density functional theory, have been carried out in order to aid in the analysis of the Raman spectrum as well as providing additional insights into the geometry and thermodynamics of the hydrogen bonds. Complementary information concerning the thermal expansion, crystal morphology and the solubility are also presented.

Crystal structure of N-(propan-2-yl-carbamo-thio-yl)benzamide

In the crystal structure of the title compound, C11H14N2OS, the six atoms of the central C2N2OS residue are coplanar (r.m.s. deviation = 0.002 Å), which facilitates the formation of an intra-molecular N-H⋯O hydrogen bond, which closes an S(6) loop. The terminal phenyl ring is inclined with respect to the central plane [dihedral angle = 42.10 (6)°]. The most prominent feature of the crystal packing is the formation of {⋯HNCS}2 synthons resulting in centrosymmetric dimers.

Crystal structure refinement with SHELXL

The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

The Diffraction Pattern Calculator (DPC) toolkit: a user-friendly approach to unit-cell lattice parameter identification of two-dimensional grazing-incidence wide-angle X-ray scattering data

The DPC toolkit is a simple-to-use computational tool that helps users identify the unit-cell lattice parameters of a crystal structure that are consistent with a set of two-dimensional grazing-incidence wide-angle X-ray scattering data. The input data requirements are minimal and easy to assemble from data sets collected with any position-sensitive detector, and the user is required to make as few initial assumptions about the crystal structure as possible. By selecting manual or automatic modes of operation, the user can either visually match the positions of the experimental and calculated reflections by individually tuning the unit-cell parameters or have the program perform this process for them. Examples that demonstrate the utility of this program include determining the lattice parameters of a polymorph of a fluorinated contorted hexabenzocoronene in a blind test and refining the lattice parameters of the thin-film phase of 5,11-bis(triethylsilylethynyl)anthradithiophene with the unit-cell dimensions of its bulk crystal structure being the initial inputs.

Structure, hydrogen bonding and thermal expansion of ammonium carbonate monohydrate

We have determined the crystal structure of ammonium carbonate monohydrate, (NH4)2CO3·H2O, using Laue single-crystal diffraction methods with pulsed neutron radiation. The crystal is orthorhombic, space group Pnma (Z = 4), with unit-cell dimensions a = 12.047 (3), b = 4.453 (1), c = 11.023 (3) Å and V = 591.3 (3) Å(3) [ρcalc = 1281.8 (7) kg m(-3)] at 10 K. The single-crystal data collected at 10 and 100 K are complemented by X-ray powder diffraction data measured from 245 to 273 K, Raman spectra measured from 80 to 263 K and an athermal zero-pressure calculation of the electronic structure and phonon spectrum carried out using density functional theory (DFT). We find no evidence of a phase transition between 10 and 273 K; above 273 K, however, the title compound transforms first to ammonium sesquicarbonate monohydrate and subsequently to ammonium bicarbonate. The crystallographic and spectroscopic data and the calculations reveal a quite strongly hydrogen-bonded structure (EHB ≃ 30-40 kJ mol(-1)), on the basis of H...O bond lengths and the topology of the electron density at the bond critical points, in which there is no free rotation of the ammonium cation at any temperature. The barrier to free rotation of the ammonium ions is estimated from the observed librational frequency to be ∼ 36 kJ mol(-1). The c-axis exhibits negative thermal expansion, but the thermal expansion behaviour of the a and b axes is ormal.

Ion permeation in K⁺ channels occurs by direct Coulomb knock-on

Potassium channels selectively conduct K(+) ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K(+) concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K(+) ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K(+) conduction. Crystallographic data are consistent with directly neighboring K(+) ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K(+) channels.

Contributions of charge-density research to medicinal chemistry

This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.

Crystal structure of magnesium selenate hepta-hydrate, MgSeO4·7H2O, from neutron time-of-flight data

MgSeO4·7H2O is isostructural with the analogous sulfate, MgSO4·7H2O, consisting of isolated [Mg(H2O)6](2+) octa-hedra and [SeO4](2-) tetra-hedra, linked by O-H⋯O hydrogen bonds, with a single inter-stitial lattice water mol-ecule. As in the sulfate, the [Mg(H2O)6](2+) coordination octa-hedron is elongated along one axis due to the tetra-hedral coordination of the two apical water mol-ecules; these have Mg-O distances of ∼2.10 Å, whereas the remaining four trigonally coordinated water mol-ecules have Mg-O distances of ∼2.05 Å. The mean Se-O bond length is 1.641 Å and is in excellent agreement with other selenates. The unit-cell volume of MgSeO4·7H2O at 10 K is 4.1% larger than that of the sulfate at 2 K, although this is not uniform; the greater part of the expansion is along the a axis of the crystal.