scholarly journals Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras

2019 ◽  
Vol 75 (2) ◽  
pp. 111-115 ◽  
Author(s):  
Ryan Knihtila ◽  
Alicia Y. Volmar ◽  
Flora Meilleur ◽  
Carla Mattos
Keyword(s):  
Single Crystal ◽  
Radiation Damage ◽  
Communication Networks ◽  
Active Site ◽  
Small Gtpase ◽  
Data Sets ◽  
Neutron Data ◽  
Major Drawback ◽  
X Ray ◽  
Ionizable Groups

Neutron protein crystallography (NPC) reveals the three-dimensional structures of proteins, including the positions of H atoms. The technique is particularly suited to elucidate ambiguous catalytic steps in complex biochemical reactions. While NPC uniquely complements biochemical assays and X-ray structural analyses by revealing the protonation states of ionizable groups at and around the active site of enzymes, the technique suffers from a major drawback: large single crystals must be grown to compensate for the relatively low flux of neutron beams. However, in addition to revealing the positions of hydrogens involved in enzyme catalysis, NPC has the advantage over X-ray crystallography that the crystals do not suffer radiation damage. The lack of radiation damage can be exploited to conduct in crystallo parametric studies. Here, the use of a single crystal of the small GTPase Ras to collect three neutron data sets at pD 8.4, 9.0 and 9.4 is reported, enabling an in crystallo titration study using NPC. In addition to revealing the behavior of titratable groups in the active site, the data sets will allow the analysis of allosteric water-mediated communication networks across the molecule, particularly regarding Cys118 and three tyrosine residues central to these networks, Tyr32, Tyr96 and Tyr137, with pK a values expected to be in the range sampled in our experiments.

scholarly journals Lower resolution Laue neutron data yield correct nanocluster formulations

2014 ◽  
Vol 70 (a1) ◽  
pp. C187-C187
Author(s):  
Alison Edwards
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Diffraction Pattern ◽  
Precise Determination ◽  
Data Sets ◽  
X Rays ◽  
Low Resolution ◽  
Neutron Data ◽  
X Ray ◽  
Product Formulation

"The renaissance in Laue studies - at neutron sources - provides us with access to single crystal neutron diffraction data for synthetic compounds without requiring synthesis of prohibitively large amounts of compound or improbably large crystals. Such neutron diffraction studies provide vital data where proof of the presence or absence of hydrogen in particular locations is required and which cannot validly be proved by X-ray studies. Since the commissioning of KOALA at OPAL in 2009[1] we have obtained numerous data sets which demonstrate the vital importance of measuring data even where the extent of the diffraction pattern is at relatively low resolution - especially when compared to that obtainable for the same compound with X-rays. In the Laue experiment performed with a fixed radius detector, data reduction is only feasible for crystals in the ""goldilocks"" zone – where the unit cell is relatively large for the detector, a correspondingly low resolution diffraction pattern in which adjacent spots are less affected by overlap will yield more data against which a structure can be refined than a pattern of higher resolution – one where neighbouring spots overlap rendering both unusable (in our current methodology). Analogous application of powder neutron diffraction in such determinations is also considered. Single crystal neutron diffraction studies of several important compounds (up to 5KDa see figure below)[2] in which precise determination of hydride content by neutron diffraction was pivotal to the final formulation will be presented. The neutron data sets typically possess 20% or fewer unique data at substantially "lower resolution" than the corresponding X-ray data sets. Careful refinement clearly reveals chemical detail which is typically unexplored in related X-ray diffraction studies reporting high profile chemistry despite the synthetic route being one which hydride ought to be considered/excluded in product formulation."

scholarly journals Rietveld refinement round robin. I. Analysis of standard X-ray and neutron data for PbSO4

1992 ◽  
Vol 25 (5) ◽  
pp. 589-610 ◽  
Author(s):  
R. J. Hill
Keyword(s):  
Single Crystal ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Analysis ◽  
Data Sets ◽  
X Rays ◽  
Neutron Data ◽  
X Ray ◽  
Atomic Coordinates

The Commission on Powder Diffraction of the International Union of Crystallography has undertaken an intercomparison of Rietveld refinements performed with two `standard' PbSO4 powder diffraction patterns: a conventional (two-wavelength) X-ray pattern collected on a Bragg–Brentano diffractometer with Cu Kα radiation and a constant-wavelength neutron pattern collected on the D1A diffractometer at the Institut Laue–Langevin. The aims of this project were: (i) to evaluate a cross section of currently used Rietveld refinement software; (ii) to examine the range and effect of various strategies of Rietveld refinement; (iii) to assess the precision and accuracy (spread) of the parameters derived by Rietveld analysis. 23 participants provided 18 refinements with the X-ray data and 20 refinements with the neutron data, using 11 different Rietveld-analysis programs. Analysis of the submitted results shows that refinement strategies play a large part in determining the detailed outcome of a Rietveld refinement. The wide variation in the values of the agreement indices obtained in these studies of the same data sets highlights the need for standardization both of the refinement procedures and of the type of data included in the algorithms used for assessing the fit. The major factors limiting the accuracy of the derived PbSO4 crystal structure parameters were: (i) use of insufficiently flexible peak shape and/or background functions; (ii) elimination of the high-angle diffraction data from the refinement; (iii) inclusion of an insufficiently wide range of diffraction angles on either side of the centroid of each peak during the step intensity calculation; and, additionally for X-rays, (iv) simultaneous release of the O-atom site-occupancy and displacement parameters. Rietveld analysis of the PbSO4 X-ray powder diffraction data provided atomic coordinates and isotropic displacement parameters for the Pb and S atoms that are precise (i.e. have small e.s.d.s) and are in reasonable agreement with the values derived from a single crystal study (viz the spread of coordinates is over the range 0.007–0.042 Å). On the other hand, the `light' O-atom parameters show relatively poor precision and have a disconcertingly wide spread of values about the weighted mean (viz 0.12–0.19 Å for the coordinates). Despite the much lower intrinsic resolution of the neutron data (i.e. peak widths some four times those of the X-ray data), the coordinates and anisotropic displacement parameters obtained for the Pb and O atoms are very precise and have a relatively narrow distribution about the single-crystal results, namely 0.004–0.020 Å for the coordinates. The range of coordinates determined from the neutron data for the relatively `light' S atom is correspondingly larger, namely 0.024–0.043 Å, about equivalent to that obtained from the X-ray data. In general, and as expected, the e.s.d.s from the Rietveld analyses are substantially smaller than the observed inter-refinement variation of the unit-cell dimensions, atomic coordinates and isotropic displacement parameters by factors of up to, respectively, 17, 5 and 22 for X-rays, and 25, 3 and 5 for neutrons. This investigation indicates that results of possibly high precision but low accuracy are not uncommon in Rietveld analysis. The disparity between individual refinements can be expected to increase further when, unlike here, the analyses are undertaken using data sets collected under diverse experimental conditions.

scholarly journals Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both

2019 ◽  
Vol 26 (4) ◽  
pp. 931-944 ◽  
Author(s):  
Helena Taberman ◽  
Charles S. Bury ◽  
Mark J. van der Woerd ◽  
Edward H. Snell ◽  
Elspeth F. Garman
Keyword(s):  
Reaction Mechanism ◽  
Radiation Damage ◽  
Xylose Isomerase ◽  
Data Sets ◽  
High Resolution Data ◽  
X Ray ◽  
Metal Cofactor ◽  
Acid Environment ◽  
Radiation Induced ◽  
Catalytic Metal

Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13–3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.

Synchrotron radiation study of yttria-stabilized zirconia, Zr0.758Y0.242O1.879

1999 ◽  
Vol 55 (5) ◽  
pp. 726-735 ◽  
Author(s):  
N. Ishizawa ◽  
Y. Matsushima ◽  
M. Hayashi ◽  
M. Ueki
Keyword(s):  
Synchrotron Radiation ◽  
Single Crystal ◽  
Yttria Stabilized Zirconia ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Stabilized Zirconia ◽  
X Ray ◽  
Ideal Position ◽  
Fluorite Type ◽  
The Ideal

The fluorite-related cubic structure of yttria-stabilized zirconia, Zr0.75 8Y0.24 2O1.87 9, has been studied by single-crystal X-ray diffraction using synchrotron radiation and by EXAFS. Two diffraction data sets obtained at X-ray energies of 512 and 10 eV below the Y K edge revealed that in the average structure Zr atoms are displaced from the origin of the space group Fm3¯m along 〈111〉 by 0.19 Å, while Y atoms reside at the origin. Approximately 48% of the O atoms occupy the ideal position in the fluorite-type structure, while 43% of O atoms are displaced from the ideal position along 〈001〉 by 0.31 Å. The remaining 9% of O atoms are presumably sited at interstitial positions. Local structures around Zr and Y are investigated by combining the results of single-crystal X-ray diffraction and EXAFS studies.

scholarly journals Removing multiple outliers and single-crystal artefacts from X-ray diffraction computed tomography data

2015 ◽  
Vol 48 (6) ◽  
pp. 1943-1955 ◽  
Author(s):  
Antonios Vamvakeros ◽  
Simon D. M. Jacques ◽  
Marco Di Michiel ◽  
Vesna Middelkoop ◽  
Christopher K. Egan ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Single Crystal ◽  
Tomographic Reconstruction ◽  
Projection Data ◽  
Data Sets ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Tomography Data

This paper reports a simple but effective filtering approach to deal with single-crystal artefacts in X-ray diffraction computed tomography (XRD-CT). In XRD-CT, large crystallites can produce spots on top of the powder diffraction rings, which, after azimuthal integration and tomographic reconstruction, lead to line/streak artefacts in the tomograms. In the simple approach presented here, the polar transform is taken of collected two-dimensional diffraction patterns followed by directional median/mean filtering prior to integration. Reconstruction of one-dimensional diffraction projection data sets treated in such a way leads to a very significant improvement in reconstructed image quality for systems that exhibit powder spottiness arising from large crystallites. This approach is not computationally heavy which is an important consideration with big data sets such as is the case with XRD-CT. The method should have application to two-dimensional X-ray diffraction data in general where such spottiness arises.

scholarly journals Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser

2019 ◽  
Vol 75 (8) ◽  
pp. 547-551 ◽  
Author(s):  
Robert J. Trachman ◽  
Jason R. Stagno ◽  
Chelsie Conrad ◽  
Christopher P. Jones ◽  
Pontus Fischer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Free Electron ◽  
Free Electron Laser ◽  
Structural Model ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Turn On

Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III–TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump–probe experiments on fluorescent RNA–small molecule complexes.

scholarly journals Single Crystal X-ray Structure Analyses of Thallides: Halide Incorporation and Mixed Alkali Sites in A8Tl11X (A = K, Rb, Cs; X = Cl, Br)

Proceedings ◽  
2018 ◽  
Vol 2 (14) ◽  
pp. 1124
Author(s):  
Stefanie Gärtner ◽  
Susanne Tiefenthaler
Keyword(s):  
Single Crystal ◽  
Alkali Metals ◽  
Data Sets ◽  
Moisture Sensitivity ◽  
Metal Compounds ◽  
X Ray ◽  
Mixed Alkali ◽  
Extra Electron ◽  
Alkali Metal Compounds ◽  
New Compounds

A8Tl11 (A = alkali metal) compounds have been known since the investigations of Corbett et al. in 1995 and still are matter of current discussions as the compound includes one extra electron referred to the charge of the Tl117− cluster. Attempts to substitute the charge by incorporation of a halide atom succeeded for the lightest homologue of the group, Cs8Ga11Cl, and powder diffraction experiments for the heavier homologues also suggested the formation of analogous compounds. However, X-ray single crystal studies on A8Tl11X to prove this substitution and to provide a deeper insight into the influence on the thallide substructure have not yet been performed, probably due to severe absorption combined with air and moisture sensitivity for this class of compounds. In our contribution we present single crystal X-ray analyses of the new compounds Cs8Tl11Cl0.8, Cs8Tl11Br0.9 and Cs5Rb3Tl11Cl0.5. It is shown that a (partial) incorporation of halide can also be indirectly determined by examination of the Tl-Tl distances for low resolved data sets, e.g., for Cs5.7K2.3Tl11Cl?. Mixed occupied sites by two different alkali metals indicate a dependence on the cesium content, the systems K/Rb–Tl–Br and K/Rb–Tl–Cl only gave rise to the formation of the higher reduced (K/Rb)8Tl11 and the less reduced by-product (K/Rb)15Tl27. We have not been able to prove the formation of halide including thallides in the absence of cesium.

Investigation into the Crystal Structure of the Perovskite Lead Hafnate, PbHfO3

1998 ◽  
Vol 54 (1) ◽  
pp. 18-28 ◽  
Author(s):  
D. L. Corker ◽  
A. M. Glazer ◽  
W. Kaminsky ◽  
R. W. Whatmore ◽  
J. Dec ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Room Temperature ◽  
Lead Zirconate ◽  
Crystal Structure Analysis ◽  
Temperature Structure ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray

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.

On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds

2018 ◽  
Vol 51 (4) ◽  
pp. 1094-1101 ◽  
Author(s):  
Yunchen Wang ◽  
Taimin Yang ◽  
Hongyi Xu ◽  
Xiaodong Zou ◽  
Wei Wan
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structural Models ◽  
Electron Diffraction Data ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Continuous Rotation

The continuous rotation electron diffraction (cRED) method has the capability of providing fast three-dimensional electron diffraction data collection on existing and future transmission electron microscopes; unknown structures could be potentially solved and refined using cRED data collected from nano- and submicrometre-sized crystals. However, structure refinements of cRED data using SHELXL often lead to relatively high R1 values when compared with those refined against single-crystal X-ray diffraction data. It is therefore necessary to analyse the quality of the structural models refined against cRED data. In this work, multiple cRED data sets collected from different crystals of an oxofluoride (FeSeO3F) and a zeolite (ZSM-5) with known structures are used to assess the data consistency and quality and, more importantly, the accuracy of the structural models refined against these data sets. An evaluation of the precision and consistency of the cRED data by examination of the statistics obtained from the data processing software DIALS is presented. It is shown that, despite the high R1 values caused by dynamical scattering and other factors, the refined atomic positions obtained from the cRED data collected for different crystals are consistent with those of the reference models refined against single-crystal X-ray diffraction data. The results serve as a reference for the quality of the cRED data and the achievable accuracy of the structural parameters.

The Crystal and Molecular Structure of Chloro-mer-Tris(dimethylphenylphosphine)-cis-dihydridoiridium(III) by X-Ray and Neutron Diffraction

1988 ◽  
Vol 41 (5) ◽  
pp. 641 ◽  
Author(s):  
GB Robertson ◽  
PA Tucker
Keyword(s):  
Molecular Structure ◽  
Neutron Diffraction ◽  
Single Crystal ◽  
Least Squares ◽  
Crystal And Molecular Structure ◽  
Monoclinic Space Group ◽  
Neutron Data ◽  
Full Matrix ◽  
Space Group ◽  
X Ray

The structure of mer-(Pme2Ph)3Cl-cis-H2IrIII (1) has been determined by single-crystal X-ray and neutron diffraction analyses. Crystals are monoclinic, space group P21, with a 11.476(4), b 14.069(5), c 8.286(3)Ǻ, β 92.45(1)° and Z 2. Full-matrix least-squares analyses converged 0.022 for 7773 X-ray data and R(F2) = 0.062 for 1538 neutron data. Ir -H [1.557(11)Ǻ trans to Cl, 1.603(10) Ǻ trans to P] and Ir -P distances [2.292(1)Ǻ trans to P, 2.328(1)Ǻ trans to H] both exhibit trans lengthening effects. Consistent with the increased hydride content the Ir -P distances in (1) are c. 0.04 Ǻ shorter than for the corresponding bonds in its dichloro monohydrido analogues and c. 0.08 Ǻ shorter than those in the trichloride . In contrast Ir-Cl [2.505(1)Ǻ] is not significantly different to the corresponding distance (2.504 Ǻ av.) in mer -(PMe2Ph)3-cis-Cl2HIrIII.

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