scholarly journals Double-flow focused liquid injector for efficient serial femtosecond crystallography

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Dominik Oberthuer ◽  
Juraj Knoška ◽  
Max O. Wiedorn ◽  
Kenneth R. Beyerlein ◽  
David A. Bushnell ◽  
...  

Abstract Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.

2016 ◽  
Vol 2 (9) ◽  
pp. e1600292 ◽  
Author(s):  
Alexander Batyuk ◽  
Lorenzo Galli ◽  
Andrii Ishchenko ◽  
Gye Won Han ◽  
Cornelius Gati ◽  
...  

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.


IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 168-176 ◽  
Author(s):  
Przemyslaw Nogly ◽  
Daniel James ◽  
Dingjie Wang ◽  
Thomas A. White ◽  
Nadia Zatsepin ◽  
...  

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.


1982 ◽  
Vol 20 ◽  
Author(s):  
R. Moret ◽  
R. Comes ◽  
G. Furdin ◽  
H. Fuzellier ◽  
F. Rousseaux

ABSTRACTIn α-C5n-HNO3 the condensation of the room-temperature liquid-like diffuse ring associated with the disorder-order transition around 250 K is studied and the low-temperature. superstructure is examined.It is found that β-C8n-HNO3 exhibits an in-plane incommensurate order at room temperature.Two types of graphite-Br2 are found. Low-temperature phase transitions in C8Br are observed at T1 ≍ 277 K and T2 ≍ 297 K. The room-temperature structure of C14Br is reexamined. Special attention is given to diffuse scattering and incommensurability.


2017 ◽  
Vol 73 (8) ◽  
pp. 702-709 ◽  
Author(s):  
Hisashi Naitow ◽  
Yoshinori Matsuura ◽  
Kensuke Tono ◽  
Yasumasa Joti ◽  
Takashi Kameshima ◽  
...  

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein–ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.


2014 ◽  
Vol 369 (1647) ◽  
pp. 20130337 ◽  
Author(s):  
Uwe Weierstall

X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques.


Barium titanium oxide, which is tetragonal at room temperature, changes about 120° C to a cubic structure. This change has been followed in detail by means of X-ray powder photo­graphs taken in a 19 cm. powder camera at intervals of a few degrees over a range covering the transition point. The unit cell, which contains the formula number of atoms, retains its identity throughout the transition, and the atomic parameters are unaltered. The change is simply in the axial lengths, and these vary continuously with the temperature, though not linearly, the varia­tion becoming more rapid near the transition point. While the linear expansion coefficients along and perpendicular to the tetrad axis are large and of opposite sign, the volume expan­sion coefficient is small and positive. There is no discontinuous change either of linear spacing or of volume detectable at the transition point, but there is a sharp discontinuity in the linear expansion coefficients, and a marked increase in the volume expansion coefficient which is probably, though not certainly, discontinuous. The transition suggests a typical λ-point change. The specific heat has not been deter­mined, but the thermal expansion curve has the characteristic λ shape. Co-existence of cubic and tetragonal structures, in proportions depending on the temperature, occurs over a range of some degrees near the transition point, and is attributed to the effect of local stresses in facilitating or hindering a change between two structures whose energy difference is very small in this temperature range. Below room temperature, observations made down to -183° C suggest that the structure may have a second transition point somewhere below this and become cubic again, the change being of the same nature as that at 120° C. It is argued that the room-temperature structure can only be explained by the existence of directed bonds, and that the breaking of these bonds with increasing temperature is respon­sible for the 120°C transition. The low-temperature transition is explained by postulating a more complete set of bonds, probably an octahedral complex, which partially breaks down at this temperature to give the square formation observed in the room-temperature structure. The possible nature of the directed bonds is discussed qualitatively. The condition which makes possible the formation of such bonds is likely to be the abnormal volume available to the Ti atom, which is due to the effect of the large Ba ion in forcing apart the oxygen lattice. The directed bond system will only contribute a small part to the attractive energy of the lattice, which is mainly ionic in character. The hypothesis that directed bonds exist, whatever their origin, is used for a tentative explanation of anomalous variations of intensity of the X-ray lines observed at temperatures near the transition point.


1994 ◽  
Vol 27 (5) ◽  
pp. 359-364 ◽  
Author(s):  
E Blanc ◽  
H.-B Bürgi ◽  
R Restori ◽  
D Schwarzenbach ◽  
P Stellberg ◽  
...  

1999 ◽  
Vol 55 (6) ◽  
pp. 886-895 ◽  
Author(s):  
Bagautdin Bagautdinov ◽  
Katrin Pilz ◽  
Jens Ludecke ◽  
Sander van Smaalen

Crystalline dicaesium mercury tetrachloride (Cs2HgCl4) is isomorphous with \beta-K_2SO_4 (space group Pnma, Z = 4) in its normal phase at room temperature. On cooling a sequence of incommensurate and commensurate superstructures occurs, below T = 221 K with modulations parallel to a*, and below 184  K with modulations along c*. The commensurately modulated structures at T = 185 K with {\bf q}= {{1}\over{5}}\bf{a}^* and at T = 176 K with {\bf q} = {{1}\over{3}}\bf{c}^* were determined using X-ray scattering with synchrotron radiation. The structure at T = 185 K has superspace group Pnma(\alpha,0,0)0ss with \alpha = 0.2. Lattice parameters were determined as a = 5\times9.7729\kern2pt(1), b = 7.5276\kern2pt(4) and c = 13.3727\kern2pt(7) Å. Structure refinements converged to R = 0.050 (R = 0.042 for 939 main reflections and R = 0.220 for 307 satellites) for the section t = 0.05 of superspace. The fivefold supercell has space group Pn2_1a. The structure at T = 176 K has superspace group Pnma(0,0,\gamma)0s0 with \gamma = {{1}\over{3}}. Lattice parameters were determined as a = 9.789\kern2pt(3), b = 7.541 \kern2pt(3) and c = 3 \times 13.418\kern2pt(4) Å. Structure refinements converged to R = 0.067 (R = 0.048 for 2130 main reflections, and R = 0.135 for 2382 satellite reflections) for the section t = 0. The threefold supercell has space group P112_1/a. It is shown that the structures of both low-temperature phases can be characterized as different superstructures of the periodic room-temperature structure. The superstructure of the 5a-modulated phase is analysed in terms of displacements of the Cs atoms, and rotations and distortions of HgCl4 tetrahedral groups. In the 3c-modulated phase the distortions of the tetrahedra are relaxed, but they are replaced by translations of the tetrahedral groups in addition to rotations.


2016 ◽  
Vol 81 (11) ◽  
pp. 1251-1262 ◽  
Author(s):  
Oluwafunmilayo Adekunle ◽  
Ray Butcher ◽  
Oladapo Bakare ◽  
Olusegun Odunola

[Cu(phen)2(CH3COO)](ClO4).2H2O (1) and [Cu(bipy)2(CH3COO)]-(ClO4).H2O (2) {phen = 1,10-phenanthroline, bipy = 2,2?-bipyridine}were synthesized and characterized. The complexes were characterized by employying elemental analyses, infrared and UV-Visible spectroscopy, room temperature magnetic measurements and the crystal structures elucidated using X-ray diffraction experiment. The redox properties of the complexes were also investigated. Both structures have a square pyramidal CuN4O chromophore which exhibit significant distortions due to long Cu-O [2.217(3) ? for (1) and 2.179 (1) for (2)] and Cu-N [2.631(2) ? for (1) and 2.714(1) ? for (2)] bonds. This distortion if further shown by the O-Cu-N bond angles [147.71(8) o for (1) and 153.40(5) o for (2)]. The elemental analyses further support the structural details unveiled by the single crystal X-ray diffraction analysis. The infrared spectra shows the acetate vibrational frequencies at 1587 cm-1,1428 cm-1, 1314 cm-1 for (1) and 1571 cm-1, 1441 cm-1, 1319c m-1 for (2) and the perchlo-rate bands at 1059 cm-1, 720 cm-1 (1) and 1080 cm-1,768 cm-1 (2). The broad d-d bands for the copper ion at 14,514 cm-1(1) and 14,535 cm-1(2) support the adoption of square pyramid geometries. The magnetic moments for the two complexes are 1.83 B.M for (1) and 1.72 B.M for (2). The peak to peak values of the two complexes show that the electrode reactions are quasi-reversibile with ?Ep = 0.023V (1) and 0.025V for (2). In both structures, there are ?-? intermolecular interactions in addition to hydrogen bonding between the units.


1998 ◽  
Vol 54 (1) ◽  
pp. 18-28 ◽  
Author(s):  
D. L. Corker ◽  
A. M. Glazer ◽  
W. Kaminsky ◽  
R. W. Whatmore ◽  
J. Dec ◽  
...  

The room-temperature crystal structure of the perovskite lead hafnate PbHfO3 is investigated using both low-temperature single crystal X-ray diffraction (Mo Kα radiation, λ = 0.71069 Å) and polycrystalline neutron diffraction (D1A instrument, ILL, λ = 1.90788 Å). Single crystal X-ray data at 100 K: space group Pbam, a = 5.856 (1), b = 11.729 (3), c = 8.212 (2) Å, V = 564.04 Å3 with Z = 8, μ = 97.2 mm−1, F(000) = 1424, final R = 0.038, wR = 0.045 over 439 reflections with F >1.4σ(F). Polycrystalline neutron data at 383 K: a = 5.8582 (3), b = 11.7224 (5), c = 8.2246 (3) Å, V = 564.80 Å3 with χ2 = 1.62. Although lead hafnate has been thought to be isostructural with lead zirconate, no complete structure determination has been reported, as crystal structure analysis in both these materials is not straightforward. One of the main difficulties encountered is the determination of the oxygen positions, as necessary information lies in extremely weak l = 2n + 1 X-ray reflections. To maximize the intensity of these reflections the X-ray data are collected at 100 K with unusually long scans, a procedure which had previously been found successful with lead zirconate. In order to establish that no phase transitions exist between room temperature and 100 K, and hence that the collected X-ray data are relevant to the room-temperature structure, birefringence measurements for both PbZrO3 and PbHfO3 are also reported.


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