scholarly journals Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

2021 ◽  
Vol 8 (4) ◽  
pp. 044701
Author(s):  
Zhen Su ◽  
Medhanjali Dasgupta ◽  
Frédéric Poitevin ◽  
Irimpan I. Mathews ◽  
Henry van den Bedem ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Atomic Displacement ◽  
Potential Utility ◽  
X Ray ◽  
Protein X ◽  
Atomic Displacement Parameters

scholarly journals Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 272
Author(s):  
Seungyeol Lee ◽  
Huifang Xu ◽  
Hongwu Xu ◽  
Joerg Neuefeind
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Single Crystal ◽  
Pair Distribution Function ◽  
Atomic Displacement ◽  
Single Crystal Xrd ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Pair ◽  
Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

scholarly journals Single-crystal neutron and X-ray diffraction study of garnet-type solid-state electrolyte Li6La3ZrTaO12: an in situ temperature-dependence investigation (2.5 ≤ T ≤ 873 K)

2021 ◽  
Vol 77 (1) ◽  
pp. 123-130
Author(s):  
Günther J. Redhammer ◽  
Martin Meven ◽  
Steffen Ganschow ◽  
Gerold Tippelt ◽  
Daniel Rettenwander
Keyword(s):  
Solid State ◽  
Single Crystal ◽  
Czochralski Method ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
Solid State Electrolyte ◽  
Cubic Symmetry ◽  
X Ray ◽  
Site Occupation ◽  
Atomic Displacement Parameters

Large single crystals of garnet-type Li6La3ZrTaO12 (LLZTO) were grown by the Czochralski method and analysed using neutron diffraction between 2.5 and 873 K in order to fully characterize the Li atom distribution, and possible Li ion mobility in this class of potential candidates for solid-state electrolyte battery material. LLZTO retains its cubic symmetry (space group Ia 3 d) over the complete temperature range. When compared to other sites, the octahedral sites behave as the most rigid unit and show the smallest increase in atomic displacement parameters and bond length. The La and Li sites show similar thermal expansion in their bond lengths with temperature, and the anisotropic and equivalent atomic displacement parameters exhibit a distinctly larger increase at temperatures above 400 K. Detailed inspection of nuclear densities at the Li1 site reveal a small but significant displacement from the 24d position to the typical 96h position, which cannot, however, be resolved from the single-crystal X-ray diffraction data. The site occupation of LiI ions on Li1 and Li2 sites remains constant, so there is no change in site occupation with temperature.

scholarly journals The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP

2021 ◽  
Vol 77 (2) ◽  
pp. 142-150
Author(s):  
Grzegorz Chojnowski ◽  
Egor Sobolev ◽  
Philipp Heuser ◽  
Victor S. Lamzin
Keyword(s):  
Main Chain ◽  
De Novo ◽  
Atomic Displacement ◽  
Test Cases ◽  
Model Accuracy ◽  
X Ray ◽  
Map Interpretation ◽  
Recent Developments ◽  
Atomic Displacement Parameters ◽  
Protein Models

Recent developments in cryogenic electron microscopy (cryo-EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high-resolution cryo-EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo-EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main-chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo-EM maps is comparable to that of X-ray crystallographic models at similar local cryo-EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.

Variation in the Einstein Temperature of Guest Atoms in Ba-Ge-X type-III Clathrate Compounds

2007 ◽  
Vol 1044 ◽  
Author(s):  
Katsushi Tanaka ◽  
Jung-Hwan Kim ◽  
Kyosuke Kishida ◽  
Haruyuki Inui
Keyword(s):  
Thermal Conductivity ◽  
Temperature Dependence ◽  
Lattice Thermal Conductivity ◽  
Atomic Displacement ◽  
X Ray ◽  
Type Iii ◽  
Clathrate Compounds ◽  
Einstein Temperature ◽  
Small Lattice ◽  
Atomic Displacement Parameters

AbstractEinstein temperatures of guest atoms in Ba-Ge-(Al, In) type-III clathrate compounds have been estimated from the temperature dependence of the atomic displacement parameters determined by synchrotron X-ray powder diffractions. The lowest temperature is obtained for the vibration of Ba(2) atoms along the x-direction, which corresponds to the “rattling motion” of the guest atoms in the compounds. The temperature estimated is significantly low of about 50 K, which agrees with the fact that the compounds have small lattice thermal conductivities of about 0.6 W/mK. Though the lattice thermal conductivity of Ba24Ge88Al12 is larger than that of Ba24Ge88In12, the Einstein temperature of Ba24Ge88Al12 is slightly smaller than that of Ba24Ge88In12. This discrepancy can be explained by the consideration of higher Debye temperature of Ba24Ge88Al12 than that of Ba24Ge88In12, that is, lattice thermal conductivity without “rattling motion” is larger for Ba24Ge88Al12 than that for Ba24Ge88In12.

scholarly journals Atomic resolution studies of carbonic anhydrase II

2010 ◽  
Vol 66 (5) ◽  
pp. 616-627 ◽  
Author(s):  
Craig A. Behnke ◽  
Isolde Le Trong ◽  
Jeff W. Godden ◽  
Ethan A. Merritt ◽  
David C. Teller ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Structural Similarity ◽  
Atomic Displacement ◽  
Atomic Resolution ◽  
Protein Surfaces ◽  
X Ray ◽  
Density Maps ◽  
Structural Details ◽  
Atomic Displacement Parameters ◽  
The Individual

Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9 Å resolution with anisotropic atomic displacement parameters to anRvalue of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25 Å) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01 Å in some zinc–protein and zinc–ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available.

scholarly journals Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data

2016 ◽  
Vol 72 (6) ◽  
pp. 770-779 ◽  
Author(s):  
Maura Malinska ◽  
Zbigniew Dauter
Keyword(s):  
Charge Density ◽  
Atomic Displacement ◽  
Coulombic Interaction ◽  
Ultrahigh Resolution ◽  
Additional Advantage ◽  
X Ray ◽  
Atom Model ◽  
Density Maps ◽  
Atomic Displacement Parameters ◽  
The University

In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules,e.g.proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventionalRfactors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

scholarly journals Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin

2012 ◽  
Vol 68 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Julian C.-H. Chen ◽  
Zoë Fisher ◽  
Andrey Y. Kovalevsky ◽  
Marat Mustyakimov ◽  
B. Leif Hanson ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Room Temperature ◽  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
Resolution Time ◽  
X Ray ◽  
Two Temperatures ◽  
Atomic Displacement Parameters

The room-temperature (RT) X-ray structure of H/D-exchanged crambin is reported at 0.85 Å resolution. As one of the very few proteins refined with anisotropic atomic displacement parameters at two temperatures, the dynamics of atoms in the RT and 100 K structures are compared. Neutron diffraction data from an H/D-exchanged crambin crystal collected at the Protein Crystallography Station (PCS) showed diffraction beyond 1.1 Å resolution. This is the highest resolution neutron diffraction reported to date for a protein crystal and will reveal important details of the anisotropic motions of H and D atoms in protein structures.

The correction of reflection intensities for incomplete absorption of high-energy X-rays in the CCD phosphor

2002 ◽  
Vol 35 (3) ◽  
pp. 356-359 ◽  
Author(s):  
G. Wu ◽  
B. L. Rodrigues ◽  
P. Coppens
Keyword(s):  
Incident Angle ◽  
Atomic Displacement ◽  
High Energy ◽  
X Rays ◽  
Structural Refinement ◽  
Data Set ◽  
X Ray ◽  
Area Detector ◽  
Angle Dependence ◽  
Atomic Displacement Parameters

It is shown that incomplete absorption of the X-ray beam in the phosphor of an area detector causes an incident-angle dependence of the recorded X-ray intensities. An energy scan of a SMART-6000 CCD (charge-coupled device) phosphor using synchrotron radiation shows the correction to be of importance above about 17 keV. Intensities of single reflections, each collected several times at different angles of incidence on the phosphor surface, show a pronounced angle-dependence at shorter wavelengths. Both conventional structural refinement and multipole charge density studies confirm that an oblique-incidence correction leads to improved quality of the results. Atomic displacement parameters will be systematically biased when the correction is not applied. For a λ = 0.394 Å data set, neglecting the correction gives rise to artifacts in the deformation density maps that are likely to lead to misinterpretation of the experimental results.

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