Combining X-ray crystallography and single-crystal spectroscopy to probe enzyme mechanisms

The combination of X-ray crystallography and rapid cryo-trapping methods has enabled the visualization of catalytic intermediates in a variety of enzyme systems. However, the resolution of the X-ray experiment is not always sufficient to precisely place the structure on the reaction pathway. In addition, many trapped intermediates are X-ray-sensitive and can decay during diffraction data collection, resulting in a final structure that may not be representative of the initial trapped species. Complementary methods, such as single-crystal spectroscopy, provide a means to precisely identify the cryo-trapped species as well as detect any X-ray-induced changes during diffraction data collection.

Download Full-text

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

Journal of Applied Crystallography ◽

10.1107/s0021889810027111 ◽

2010 ◽

Vol 43 (5) ◽

pp. 1113-1120 ◽

Cited By ~ 1

Author(s):

Esko Oksanen ◽

François Dauvergne ◽

Adrian Goldman ◽

Monika Budayova-Spano

Keyword(s):

Data Collection ◽

Neutron Diffraction ◽

Diffraction Data ◽

Catalytic Mechanism ◽

Inorganic Pyrophosphatase ◽

Neutron Diffraction Data ◽

Cooling Device ◽

Data Set ◽

X Ray ◽

X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

Download Full-text

The structure of cubic MOF [{Ca(H2O)6}{CaGd(oxydiacetate)3}2].4H2O. A comparison between structural models obtained from Rietveld refinement of conventional and synchrotron X-ray powder diffraction data and standard refinement of single-crystal X-ray diffraction data

Powder Diffraction ◽

10.1017/s0885715612000681 ◽

2012 ◽

Vol 27 (4) ◽

pp. 232-242 ◽

Cited By ~ 4

Author(s):

Leopoldo Suescun ◽

Jun Wang ◽

Ricardo Faccio ◽

Guzmán Peinado ◽

Julia Torres ◽

...

Keyword(s):

Data Collection ◽

Single Crystal ◽

Powder Diffraction ◽

Diffraction Data ◽

Structural Models ◽

Initial Time ◽

High Symmetry ◽

Powder Diffraction Data ◽

X Ray Diffraction ◽

X Ray

The structure of the metal–organic framework (MOF) compound [{Ca(H2O)6}{CaGd(oxydiacetate)3}2]·4H2O was determined by single-crystal X-ray diffraction and refined using conventional single-crystal X-ray diffraction data. In addition, the structure was refined using powder diffraction data collected from two sources, a conventional X-ray diffractometer in Bragg–Brentano geometry and a 12-detector high resolution synchrotron-based diffractometer in transmission geometry. Data from the latter were processed in three different ways to account for crystalline decay or radiation damage. One dataset was obtained by averaging the multiple detector patterns, another dataset was obtained by cutting the non-overlapping portions of each detector to consider only the first few minutes of data collection and a dose-corrected dataset was obtained by fitting the independent peaks in every dataset and extrapolating the intensity and peak position to the initial time of data collection or to zero-absorbed dose. The compared structural models obtained show that special processing of powder diffraction data produced a much accurate model, close to the single-crystal-based model for this particular compound with heavy atoms in high symmetry positions that do not contribute to a significant number of diffraction intensities.

Download Full-text

Simple pressure cell for single-crystal X-ray crystallography

Journal of Applied Crystallography ◽

10.1107/s0021889805011258 ◽

2005 ◽

Vol 38 (4) ◽

pp. 583-586 ◽

Cited By ~ 27

Author(s):

Dmitry S. Yufit ◽

Judith A. K. Howard

Keyword(s):

Data Collection ◽

Single Crystal ◽

X Ray ◽

X Ray Crystallography ◽

Pressure Cell ◽

Special Attachment ◽

Data Collection Procedure

A simple pressure cell for single-crystal X-ray crystallography at pressures up to 1 kbar (105 kPa) has been developed. A special attachment for mounting the cell onto a goniometer and a new data collection procedure are described.

Download Full-text

From then till now: changing data collection methods in single crystal X-ray crystallography since 1912

Crystallography Reviews ◽

10.1080/0889311x.2019.1615483 ◽

2019 ◽

Vol 25 (4) ◽

pp. 264-294 ◽

Cited By ~ 4

Author(s):

Harold R. Powell

Keyword(s):

Data Collection ◽

Single Crystal ◽

X Ray ◽

Data Collection Methods ◽

X Ray Crystallography ◽

Collection Methods

Download Full-text

Practical macromolecular cryocrystallography

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x15008304 ◽

2015 ◽

Vol 71 (6) ◽

pp. 622-642 ◽

Cited By ~ 28

Author(s):

J. W. Pflugrath

Keyword(s):

Glass Transition ◽

Data Collection ◽

Single Crystal ◽

Radiation Damage ◽

Diffraction Data ◽

Cryogenic Temperatures ◽

X Ray Diffraction ◽

X Ray ◽

Flash Cooling ◽

Solvent Fraction

Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.

Download Full-text

Single-crystal investigation of Ce5AgxGe4−x (x = 0.1−1.08) with Sm5Ge4 type

Zeitschrift für Naturforschung B ◽

10.1515/znb-2020-0091 ◽

2020 ◽

Vol 75 (8) ◽

pp. 765-768

Author(s):

Bohdana Belan ◽

Dorota Kowalska ◽

Mariya Dzevenko ◽

Mykola Manyako ◽

Roman Gladyshevskii

Keyword(s):

Crystal Structure ◽

Single Crystal ◽

Diffraction Data ◽

Binary Compound ◽

Lattice Parameters ◽

X Ray Diffraction ◽

Space Group ◽

X Ray

AbstractThe crystal structure of the phase Ce5AgxGe4−x (x = 0.1−1.08) has been determined using single-crystal X-ray diffraction data for Ce5Ag0.1Ge3.9. This phase is isotypic with Sm5Ge4: space group Pnma (No. 62), Pearson code oP36, Z = 4, a = 7.9632(2), b = 15.2693(5), c = 8.0803(2) Å; R1 = 0.0261, wR2 = 0.0460, 1428 F2 values and 48 variables. The two crystallographic positions 8d and 4c show Ge/Ag mixing, leading to a slight increase in the lattice parameters as compared to those of the pure binary compound Ce5Ge4.

Download Full-text

Verfeinerung der Kristallstruktur von Tripalladium-di-tetrathiophospliat Pd3(PS4)2 Refinement of the Crystal Structure of Tripalladium-di-tetrathiophosphate Pda3(PS4)2

Zeitschrift für Naturforschung B ◽

10.1515/znb-1983-0404 ◽

1983 ◽

Vol 38 (4) ◽

pp. 426-427 ◽

Cited By ~ 11

Author(s):

Arndt Simon ◽

Karl Peters ◽

Harry Hahn

Keyword(s):

Crystal Structure ◽

Single Crystal ◽

Title Compound ◽

Type Structure ◽

Tetrahedral Symmetry ◽

X Ray ◽

X Ray Crystallography ◽

Planar Environment

Abstract The structure of the title compound has been determined by X-ray crystallography. The title compound is synthesized from the elements at 600 °C. Its crystal structure, derived from powder data [3] is refined by single crystal diffractometer data. The structure is trigonal (P3̅ml, α = 684.1(1), c = 724.4(1) pm); Pd2+ cations and PS43- anions form a network with an anti-Claudetite (AS2O3) type structure. The PS4 units are distinctly distorted from ideal tetrahedral symmetry. The Pd atoms have a planar environment of 4 S atoms.

Download Full-text

The modulated structure of Bi2Sr3−xCaxCu2O8: A commensurate model from single crystal X-ray diffraction data

Physica C Superconductivity ◽

10.1016/0921-4534(89)90396-1 ◽

1989 ◽

Vol 161 (5-6) ◽

pp. 598-606 ◽

Cited By ~ 49

Author(s):

G. Calestani ◽

C. Rizzoli ◽

M.G. Francesconi ◽

G.D. Andreetti

Keyword(s):

Single Crystal ◽

Diffraction Data ◽

X Ray Diffraction ◽

Modulated Structure ◽

X Ray

Download Full-text

Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520616017534 ◽

2017 ◽

Vol 73 (1) ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Anatoly A. Udovenko ◽

Alexander A. Karabtsov ◽

Natalia M. Laptash

Keyword(s):

Single Crystal ◽

Electron Density ◽

Diffraction Data ◽

Central Atom ◽

X Ray Diffraction ◽

Dynamic Nature ◽

Orientational Disorder ◽

High Quality ◽

Structural Units ◽

X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

Download Full-text