Refinement Of Atomic Coordinates Research Articles

Modeling Ligands into Maps Derived from Electron Cryomicroscopy.

Deciphering the protein-ligand interactions in a macromolecular complex is crucial for understanding the molecular mechanism, underlying biological processes, and drug development. In recent years, cryogenic sample electron microscopy (cryoEM) has emerged as a powerful technique to determine the structures of macromolecules and to investigate the mode of ligand binding at near-atomic resolution. Identifying and modeling non-protein molecules in cryoEM maps is often challenging due to anisotropic resolution across the molecule of interest and inherent noise in the data. In this article, the readers are introduced to various software and methods currently used for ligand identification, model building, and refinement of atomic coordinates using selected macromolecules. One of the simplest ways to identify the presence of a ligand, as illustrated with the enolase enzyme, is to subtract the two maps obtained with and without the ligand. The extra density of the ligand is likely to stand out in the difference map even at a higher threshold. There are instances, as shown in the case of metabotropic Glutamate receptor mGlu5, when such simple difference maps cannot be generated. The recently introduced method of deriving the Fo-Fc omit map can serve as a tool for validating and demonstrating the presence of the ligand. Finally, using the well-studied β-galactosidase as an example, the effect of resolution on modeling the ligands and solvent molecules in cryoEM maps is analyzed, and an outlook on how cryoEM can be used in drug discovery is presented.

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM; Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-H...O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

Faster calculation of the full matrix for least-squares refinement.

Equations derived from a statistical model and valid for all space groups give estimates of the elements of the matrix for least-squares refinement of atomic coordinates and isotropic thermal parameters for a large crystal structure with many diffraction data. The elements are functions of the lengths and directions of Patterson vectors and the distribution of weights as a function of Bragg angle. For a large data set, this matrix, or a portion of it, can be calculated in a time that is approximately proportional to the number of elements calculated and independent of the number of reflections.

ChemInform Abstract: Crystal Structure of the Microwave Dielectric Resonator Ba2Ti9O20.

AbstractWie Röntgen‐ Einkristalluntersuchungen zeigen, kristallisiert die Titelverbindung in der Raumgruppe Pl mit Z=4.

Crystal Structure of the Microwave Dielectric Resonator Ba2Ti9O20

A single-crystal X-ray study of dibarium nonatitanate, Ba2Ti9O20, yielded the triclinic space group P 1 with a=0.7471(1), b= 1.4081(2), c= 1.4344(2) nm, α=89.94(2)°, β= 79.43(2)°, γ= 84.45(2)°, V = 1.476 nm3 Z = 4, and Dx= 4.61 Mg/m3. A refinement of atomic coordinates and isotropic thermal parameters led to a residual of 0.03. The structure consists of hexagonally closest-packed layers of Ba and O atoms in the sequence (hch)3. All Ti atoms reside in octahedral interstices of this closest packing. The various Ti coordination octahedra share only edges and corners with each other. One-half of the Ba atoms is twelve-coordinated by oxygen atoms, the other half is eleven-coordinated.

Eine „Phasenverfeinerung“ in der Kristallstrukturanalyse

A refinement for phases in crystal structures after the method of least squares is developed, and the formal analogy with the refinement of atomic coordinates is emphasized.

The crystal structure of ethylene carbonate

The structure of crystalline ethylene carbonate has been determined by the X-ray method. The dimensions of the monoclinic unit cell, which contains four molecules of (CH2) ~. COs, are a ---8.92, b = 6.25, c = 6.94 A, fl = 100-5 °. The space group is C2/c. X-ray intensity data were obtained from Weissenberg moving-film photographs for all layers of the three principal axes, and structure amplitudes were deduced for 372 ~separate planes. The approximate structure was derived by means of Patterson F ~ syntheses, and refinement of atomic coordinates was achieved by successive three-dimensional Fourier syntheses. The five-membered dioxalan ring is not planar, but the molecule possesses a twofold axis of symmetry which coincides with the twofold axis of symmetry in the unit cell. Although the other bond lengths are approximately normal, those associated with the COa group are somewhat shorter than were expected, C ~-O being 1.15 _~ and C--O 1-33 A.