Antoine M. M. Schreurs

An intensity evaluation method: EVAL-14

A reflection intensity integration method is presented based upon ab initio calculation of three-dimensional (x, y, ω) reflection boundaries from a few physical crystal and instrument parameters. It is especially useful in challenging circumstances, such as the case of a crystal that is far from spherical, anisotropic mosaicity, α1α2 peak splitting, interference from close neighbours, twin lattices or satellite reflections, and the case of streaks from modulated structures, all of which may frustrate the customary profile-learning and -fitting procedures. The method, called EVAL-14, has been implemented and extensively tested on a Bruker Nonius KappaCCD diffractometer.

EVAL15: a diffraction data integration method based on ab initio predicted profiles

A novel diffraction data integration method is presented, EVAL15, based upon ab initio calculation of three-dimensional (x, y, ω) reflection profiles from a few physical crystal and instrument parameters. Net intensities are obtained by least-squares fitting the observed profile with the calculated standard using singular value decomposition. This paper shows that profiles can be predicted satisfactorily and that accurate intensities are obtained. The detailed profile analysis has the additional advantage that specific physical properties of the crystal are revealed. The EVAL15 method is particularly useful in circumstances where other programs fail, such as regions of reciprocal space with weak scattering, crystals with anisotropic shape or anisotropic mosaicity, Kα1/Kα2 peak splitting, interference from close neighbours, twin lattices, or satellite reflections of modulated structures, all of which may frustrate the customary profile learning and fitting procedures. EVAL15 allows the deconvolution of overlapping reflections.

Solvent behaviour in flash-cooled protein crystals at cryogenic temperatures

The solvent behaviour of flash-cooled protein crystals was studied in the range 100--180 K by X-ray diffraction. If the solvent is within large channels it crystallizes at 155 K, as identified by a sharp change in the increase of unit-cell volume upon temperature increase. In contrast, if a similar amount of solvent is confined to narrow channels and/or individual cavities it does not crystallize in the studied temperature range. It is concluded that the solvent in large channels behaves similarly to bulk water, whereas when confined to narrow channels it is mainly protein-associated. The analogy with the behaviour of pure bulk water provides circumstantial evidence that only solvent in large channels undergoes a glass transition in the 100--180 K temperature range. These studies reveal that flash-cooled protein crystals are arrested in a metastable state up to at least 155 K, thus providing an upper temperature limit for their storage and handling. The results are pertinent to the development of rational crystal annealing procedures and to the study of temperature-dependent radiation damage to proteins. Furthermore, they suggest an experimental paradigm for studying the correlation between solvent behaviour, protein dynamics and protein function.

Weak hydrogen bonding. Part 5. Experimental evidence for the long-range nature of CC–H ⋯π interactions: crystallographic and spectroscopic studies of three terminal alkynes

In the crystal structures of three terminal alkynes, long CC–H ⋯ CC contacts with H ⋯ C separations in the range 2.7–3.1 A are observed. Despite the long distances, these contacts possess the characteristic infrared spectroscopic features of weak hydrogen bonds. This provides direct evidence that the range of C–H ⋯π interactions donated by sufficiently acidic C–H groups extends beyond van der Waals separation. In two of the crystal structures, the C–H ⋯π interactions form interconnected systems CC–H ⋯ CC–H ⋯ CC–H.

Dinuclear silver(I) and copper(I) complexes with neutral N2S2 donor ligands and their reactivities towards CO. Structure in solution (1H and INEPT 109Ag NMR) and in the solid (X-ray) of [Ag{m-(R),(S)-1,2-(thiophene-2-CH=N)2-cyclohexane}2] (O3SCF3)2

Abstract The 1/1 reactions of the neutral N2S2 donor system (R)(S)-1,2-(5-R–thiophene-2-CHN)2–cyclohexane (R = H, 1a or Me, 1b) with [M(O3SCF3)] [M = Ag(I) or Cu(I)] yielded ionic complexes, consisting of a dinuclear [M2(1)2]2+ dication and O3SCF3− monoanions. An X-ray crystallographic study characterized the molecular structure of [Ag2–(1a)2](O3SCF3)2, in the monoclinic unit cell, space group P21/n, with Z = 4; a = 17.26(1), b = 15.08(2), c = 19.960(17) A, β = 106.15(4)°, V = 4991 A3. The structure was refined to R is 0.0704. The two N2S2 ligands coor- dinate to the silver(I) centres in a bridging di- bidentate manner with short AgN(imine) [e.g. Ag(1)N(2), 2.152(10); Ag(1)N(7), 2.162(9); Ag(2)N(3), 2.153(10); Ag(2)N(6), 2.158(10) A] and long AgS(thiophene) distances [Ag(1)S(1), 2.961(4); Ag(1)S(8), 2.938(4); Ag(2)S(4), 2.928(4); Ag(2)S(5), 2.995(5) A]. The Ag(1) Ag(I) separation is 2.909(1) A. In solution the coordination properties of the N2S2 ligands to silver(I) and copper(I) have been studied by 1H and INEPT 109Ag NMR spectroscopy. The 1H NMR data revealed, by the presence of two thiophene–imine 1H patterns at 190 K, that at this temperature i) the structural features found for [Ag2(1a)2]2+ in the solid are retained in solution and ii) the silver(I) and copper(I) complexes have similar structures in solution. Furthermore, the presence of 3J(1H107,109Ag) on the imine-H resonances of the silver(I) complexes indicates that at 190 K intermolecular exchange processes are slow on the NMR time scale. From the difference in δ109Ag of the [Ag2(1)2](O3SCF3)2 complexes, R = H (δ + 678) or Me (δ + 659), it was concluded that weak thiopheneSAg(I) interactions are present, and stabilize the formation of the [M2(1)2]2+ dications. However, in the reversible reactions of [Cu2(1)2](O3SCF3)2 with carbon monoxide the thiopheneSCu(I) bonds dissociate and neutral complexes are formed having a [{CuCO(O3SCF3)}2{μ−1}2] type of structure. In these complexes both the carbon monoxide and OSO2CF3 groups are terminally coordinated to Cu(I) (R = H, ν(CO), 2089 cm−1; R = Me, ν(CO) = 2087 cm−1 in CH2Cl2).

Room-temperature X-ray diffraction studies of cisplatin and carboplatin binding to His15 of HEWL after prolonged chemical exposure.

The anticancer complexes cisplatin and carboplatin are known to bind to both the Nδ and the Nℇ atoms of His15 of hen egg-white lysozyme (HEWL) in the presence of dimethyl sulfoxide (DMSO). However, neither binds in aqueous media after 4 d of crystallization and crystal growth, suggesting that DMSO facilitates cisplatin/carboplatin binding to the N atoms of His15 by an unknown mechanism. Crystals of HEWL cocrystallized with cisplatin in both aqueous and DMSO media, of HEWL cocrystallized with carboplatin in DMSO medium and of HEWL cocrystallized with cisplatin and N-acetylglucosamine (NAG) in DMSO medium were stored for between seven and 15 months. X-ray diffraction studies of these crystals were carried out on a Bruker APEX II home-source diffractometer at room temperature. Room-temperature X-ray diffraction data collection removed the need for cryoprotectants to be used, ruling out any effect that the cryoprotectants might have had on binding to the protein. Both cisplatin and carboplatin still bind to both the Nδ and Nℇ atoms of His15 in DMSO media as expected, but more detail for the cyclobutanedicarboxylate (CBDC) moiety of carboplatin was observed at the Nℇ binding site. However, two molecules of cisplatin were now observed to be bound to His15 in aqueous conditions. The platinum peak positions were identified using anomalous difference electron-density maps as a cross-check with Fo-Fc OMIT electron-density maps. The occupancies of each binding site were calculated using SHELXTL. These results show that over time cisplatin binds to both N atoms of His15 of HEWL in aqueous media, whereas this binding is speeded up in the presence of DMSO. The implication of cisplatin binding to proteins after a prolonged period of time is an important consideration for the length of treatment in patients who are given cisplatin.

Supercooled liquid-like solvent in trypsin crystals: implications for crystal annealing and temperature-controlled X-ray radiation damage studies

The study of temperature-dependent physical changes in flash-cooled macromolecular crystals is pertinent to cryocrystallography and related issues such as crystal annealing, X-ray radiation damage and kinetic crystallography. In this context, the unit-cell volume of flash-cooled trigonal and orthorhombic trypsin crystals has been monitored upon warming from 100 to 200 K and subsequent re-cooling to 100 K. Crystals of both forms were obtained under the same crystallization conditions, yet they differ in solvent content and channel size. An abrupt non-reversible unit-cell volume decrease is observed at 185 K in orthorhombic and at 195 K in trigonal crystals as the temperature is increased; this result is consistent with ultra-viscous solvent leaving the crystals. Concomitant appearance of ice rings in the diffraction patterns suggests that the transported solvent forms crystalline ice. These results demonstrate that solvent in flash-cooled protein crystals is liquid-like near its crystallization temperature, as has been proposed, yet controversially discussed, for the case of pure water. The use of mineral oil prevents the unit-cell volume decrease in trigonal but not in orthorhombic crystals. The observation of liquid-like solvent has implications in the development of annealing protocols and points a way to the rational design of temperature-controlled crystallographic studies that aim either at studying specific radiation damage or at trapping enzymatic intermediate states.

Water Molecules Hydrogen Bonding to Aromatic Acceptors of Amino Acids: the Structure of Tyr-Tyr-Phe Dihydrate and a Crystallographic Database Study on Peptides

The crystal structure of Tyr-Tyr-Phe dihydrate contains a hydrogen bond formed between a water molecule and the Phe side chain. The geometry is centered with a distance of 3.26 A between the water O atom and the aromatic centroid. In a database study on hydrated peptides, four related examples are found which exhibit a wide variability of hydrogen-bond geometries. The intermolecular surroundings of the water molecules are inspected, showing that they are typically involved in complex networks of conventional and non-conventional hydrogen bonds. Possible relevance for protein hydration is given.

Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals

A systematic analysis of diffraction data of 11 different lysozyme crystals (used for cisplatin and carboplatin binding studies), obtained with four diffraction data processing software packages and from two different diffractometers, serves as a pilot study for archiving raw diffraction data and associated metadata. The availability of the raw diffraction images allows for independent assessment of software packages.

Experiences with archived raw diffraction images data : capturing cisplatin after chemical conversion of carboplatin in high salt conditions for a protein crystal

Archiving of raw diffraction images data has led to new structural chemistry information being obtained for previously published results, which leads to the conclusion that carboplatin has partially converted to cisplatin in the high NaCl concentration conditions used in the crystallization procedure.