Polycapillary optic–source combinations for protein crystallography

The work in this paper is a systematic study of the application of collimating and slightly focusing polycapillary optics to the X-ray crystallographic structure determination of egg-white lysozyme using two different sources: a standard rotating anode source and a low-power table-top microfocusing source. For the rotating anode source, a series of measurements comparing duplicate data sets obtained from the same individual crystal are summarized. Intensity and data quality are discussed for measurements with a pinhole collimator, a collimating polycapillary optic and a focusing polycapillary optic. The collected data were analyzed using conventional analysis software; limitations of the use of conventional analysis software for focused beams are discussed. Two data sets were collected using the low-power source and collimating optics, and three data sets using a lower-power source and focusing optics with three different limiting apertures.

Stationary crystal diffraction with a monochromatic convergent X-ray source and application for macromolecular crystal data collection

A diffraction geometry utilizing convergent X-rays from a polycapillary optic incident on a stationary crystal is described. A mathematical simulation of the resulting diffraction pattern (in terms of spot shape, position and intensity) is presented along with preliminary experimental results recorded from a lysozyme crystal. The effective source coverage factor is introduced to bring the reflection intensities onto the same scale. The feasibility of its application to macromolecular crystal data collection is discussed.

Effects of H/D substitution on thermal vibrations in piperazinium hexanoate-h11, d11

The crystal structures of piperazinium hexanoate-h11, 1/2C4H12N2(2+).C6H11O2-, and piperazinium hexanoate-d11, 1/2C4H12N2(2+).C6D11O2-, have been determined from neutron diffraction data collected at 15 K. Nuclear anisotropic displacement parameters have been analyzed to obtain the internal molecular displacements of the H and D nuclei, given by (u(obs)2)-(u(ext)2) where (u(ext)2) is the contribution assuming all H/D to be carried rigidly on the vibrating molecular framework consisting of the heavier nuclei. In both crystal structures the cation ring is well fitted by the rigid-body model and the anion chain by a model with two rigid segments. In the piperazinium cations the corresponding protons in the two structures have about the same internal vibrational directions and magnitudes except for the two N--H protons, perhaps owing to differences in N--H...O hydrogen bonding. The internal vibrations of corresponding H/D in the h11 and d11 anions have approximately the same vibrational directions. The internal mean-square displacements of the H nuclei are systematically greater than the values of the corresponding D nuclei by an average factor 1.7(3). For both anions, normal-mode analyses have been carried out using the force fields derived from ab initio quantum-mechanical calculations with HF/3-21G and HF/6-31G** basis sets. The values of the resultant H/D internal displacements for C--H(D) bond stretching and methylene out-of-plane vibrations are in good agreement with experiment. However, with either basis set, theory predicts methylene in-plane mean-square displacements significantly greater than the experimental values.

Crystal structure of piperazinium oleate at -150 degrees C

The crystal structure of piperazinium oleate ([C4H12N2]2+.2[C18H34O2]-) has been determined from X-ray diffraction data at -150 degrees C in order to study the oleate chain conformation and molecular packing. Differential scanning calorimetry shows three reversible crystalline state phase transitions (54.5, -34.8, and -54.8 degrees C) in the range from the melting point (84.8 degrees C) to -160 degrees C. The cell constants for a flash-frozen crystal at -150 degrees C are a = 5.630(2), b = 14.900(2), c = 24.825(4) A, alpha = 88.77(2), beta = 88.12(2), gamma = 80.38(2) degrees; Z = 2, space group P1; Dc = 1.05 g cm-3, m.p. = 84.8 degrees C. The cell constants are similar at room temperature except for a doubling of b at -150 degrees C. The crystal structure at -150 degrees C has been refined to R(F2) = 0.116 for 8410 independent reflections. There are two independent oleate anions (A and B), both having an overall extended conformation except for kinks that are different at the cis olefin group. The oleate A chain is ordered while the oleate B chain is disordered in two regions. Because of different torsion angles at bonds adjacent to the double bond, the B-chain olefin group adopts two configurations, one of which is predominant. From the olefin group to the terminal methyl group, the B-chain adopts one of two all-trans configurations with equal probability. It cannot be determined whether the two kinds of disorder are correlated. Taking into account the centrosymmetrically related oleate chains, the crystal structure contains at least six and possibly eight extended chain conformers with different kinks at the olefin group. Third and fourth order displacement parameters have been determined for the partially resolved atomic sites in the oleate B chain and these have been used to map probability density functions for the disordered atoms. The piperazinium cations are in a chair conformation. Each is hydrogen bonded to four oleate anions, forming an infinite ribbon parallel to (025). These ribbons are stacked upon each other to form a monolayer 24.8 A thick parallel to (001).

The charge-density distribution in hexamethylenetetramine at 120 K

The charge-density distribution has been determined from 333 independent X-ray reflections with sin theta/lambda < 1.47 A-1, which were collected with Ag K alpha radiation. As found in a recent refinement using room-temperature data, full-matrix least squares refinement with a multipole model gives rise to an almost complete correlation between certain octapole deformation terms. This is the worst case example of a problem which will always arise to some degree when applying the multipole model in a noncentrosymmetric space group. In this example, the correlation arises between terms which are predominant for describing the bonding density between atoms of the molecule, thereby causing the deformation charge density to have little meaning. However, the total molecular electrostatic potential and the molecular octapole moment are reliably obtained.

The crystal structure of 1,2-dipalmitoyl-sn-glycerol at 123 K

At 123 K, the crystal structure of 1,2-dipalmitoyl-sn-glycerol (C35H68O5, M(r) = 568.9) is monoclinic with space group P2(1), a = 5.480(1), b = 7.301(1), c = 43.145(7) A, beta = 92.91(1) degrees, V = 1724 A3, Dc = 1.0960 g cm-3 and Z = 2. Integrated X-ray intensities for 3574 independent reflections were measured with Ni-filtered Cu-K alpha radiation (lambda = 1.5418 A, mu = 0.56 mm-1), and these were all used in a full-matrix least-squares refinement which gave R(F2) = 0.142. Bond lengths and angles have e.s.d.s less than 0.01 A and 0.1 degrees for non-hydrogen atoms. Comparison with a previously reported study of the room temperature structure shows a very similar orthorhombic mode of chain packing but significant conformational differences in the polar headgroup. These changes may occur in conjunction with small changes in enthalpy (less than 1 kJ/mol) observed at 202, 193 and 136 K and with a discontinuity in the unit cell volume observed in the range 200-190 K. Analysis of the atomic mean square displacements at 123 K indicates the presence of internal torsional vibrations in the headgroup region that involve the carbonyl and hydroxyl O-atoms.

Structure and thermal vibrations of adenosine from neutron diffraction data at 123 K

The crystal structure of adenosine, C10H13N5O4, Mr = 267.24, has been refined by full-matrix least-squares methods using single-crystal neutron diffraction data (sin theta/lambda less than 0.79 A-1) measured at 123 K. Crystal data at 123 K: monoclinic, P2l, Z = 2, a = 4.7885 (8), b = 10.240 (2), c = 11.772 (2) A, beta = 99.59 (2) degrees, V = 569.2 A3, lambda = 1.0402 (1) A, Dn = 1.559 Mg m-3, mu = 191.1 m-1, F(000) = 175.72 fm, R(F2) = 0.044, wR(F2) = 0.055, S = 1.13 for 2450 reflections with F2 greater than 0.0. Bond lengths and angles have e.s.d.'s less than 0.002 A and 0.1 degrees for non-H atoms and less than 0.004 A and 0.3 degrees for H atoms. Values are in general agreement with those previously obtained from room-temperature X-ray data and with those obtained for 9-methyladenine by neutron diffraction at 126 K. Small displacements of amino H atoms from the least-squares plane through the non-H atoms of the adenine part appear to be the result of hydrogen bonding. There is an intermolecular interaction C2--H2...O2' with an H...O distance of 2.20 A. In its thermal vibrations, the adenosine molecule behaves as two rigid segments with a torsional libration about the glycosidic bond of 14.4 deg2 at 123 K. The force constant for this libration, as determined from the diffraction data, is 73 (10) J mol-1 deg-2.

The crystal structure of isobutyl 2,3,4-tri-O-acetyl-1-thio-beta-D-xylopyranoside

Isobutyl 2,3,4-tri-O-acetyl-1-thio-beta-D-xylopyranoside is monoclinic, P21, with a = 10.134(4), b = 7.748(3), c = 11.726(4) A, beta = 96.63(3) degrees, V = 914.55 A3, Z = 2, Dm = 1.262, Dx = 1.264 g . cm-3, mu(MoK alpha) = 226 M-1. The X-ray intensities of 1724 reflections were measured with Nb-filtered MoK alpha radiation (lambda = 0.7107 A) at room temperature. The structure was solved by direct methods, and refined by full-matrix least squares, with anisotropic thermal parameters for the carbon and oxygen atoms and isotropic thermal parameters for the hydrogen atoms, to a final agreement factor of R = 0.08. The molecule has the 4C1(D) conformation, with puckering parameters Q = 0.582 A, theta = 5.6 degrees, phi = 334.7 degrees. The acetyl groups have the planar, (S)-cis configuration most commonly observed. They are oriented, as in many other per-O-acetylated aldopyranosides, with the acetyl planes within +/- 30 degrees of the C-H bond at the ring-carbon atom to which they are attached. Although this is primarily a van der Waals structure, there is some evidence for CH---O hydrogen-bonding.

Crystal structure of beta-D-galactopyranosylamine

The crystal structure of beta-D-galactopyranosylamine (C6H13O5N) is orthorhombic, with space group P2(1)2(1)2(1), and cell dimensions a = 7.703(2), b = 7.788(2), c = 12.645(3) A, V = 757.612 A3, Z = 4; Dc and Dm are 1.573 and 1.587 cm-3, respectively. Using MoK alpha radiation (lambda = 0.7107 A), 2841 reflections were measured on a CAD-4 diffractometer. The structure was solved by using MULTAN-78, and refined anisotropically for the non-hydrogen positional and thermal parameters. Final agreement indices are R(F) = 0.074, wR(F) = 0.086, and S = 2.1523. The conformation is 4C1(D). The orientation of the primary alcohol group is gauche/trans. An unexpected feature of the hydrogen bonding is that the amino group accepts a strong O-H---N bond, but has no donor functionality in the crystal structure.

The crystal structure of ethyl 2,3-dideoxy-α-d-erythro-hex-2-enopyranoside

The crystal structure of ethyl 2,3-dideoxy-alpha-D-erythro-hex-2-enopyranoside, C8H14O4, is orthorhombic, P2(1)2(1)2(1), with cell dimensions at 123 K [293 K] a = 11.220(2) [11.319(1)], b = 18.387(3) [18.458(2)], c = 8.509(2) [8.635(1)] A, Z = 8. There are two symmetry-independent molecules in the asymmetric unit. In both molecules, the conformation is oH5. The alkenic bond is almost exactly planar in one molecule, with C-1--C-2--C-3--C-4 = +0.8 degrees. In the other molecule, this torsion angle is +3.7 degrees. The glycosidic torsion angle, O-5--C-1--O-1--C-7, has normal exoanomeric values of +71 and +64 degrees. The conformation of the ethoxyl group is extended, with C-1--O-1--C-7--C-8 = +162 and +170 degrees. The primary alcohol group has different orientations, g/t on one molecule, g/g on the other. The characteristic glycosidic bond-shortening observed in the pyranosides is modified in this enopyranoside. Both the ring bond, O-5--C-1, and the glycosidic bond, C-1--O-1, are short, with distances ranging from 1.409 to 1.425 A. Solution and solid-state c.p.-m.a.s., 13C-n.m.r. spectra are reported.