Correction to Crystal Structure of Poly(7-heptalactone)
Ontology highlight
ABSTRACT:
SUBMITTER:
PROVIDER: S-EPMC10413960 | biostudies-literature | 2023 Jul
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:[This corrects the article DOI: 10.1021/acscentsci.0c00426.].
| S-EPMC8949623 | biostudies-literature
Project description:Previously published crystal structure determinations of two modifications of iodine azide (IN3 ) are corrected. In the original determinations, the very weak X-ray reflections with odd k Miller indices had been discarded, resulting in too small unit cells and models with misordered, partly occupied atomic positions. Using the original diffraction data, refinements with the correct unit cells yield structures of polymeric (-I-N3 -)n chains that are interlocked to layers. A skilled look at the primary X-ray data is always recommended to overcome the lack of crystallographic expertise of computers at automated structure determinations.
| S-EPMC8361933 | biostudies-literature
Project description:Correcting for anomalous dispersion is part of any refinement of an X-ray dif-fraction crystal structure determination. The procedure takes the inelastic scattering in the diffraction experiment into account. This X-ray absorption effect is specific to each chemical compound and is particularly sensitive to radiation energies in the region of the absorption edges of the elements in the compound. Therefore, the widely used tabulated values for these corrections can only be approximations as they are based on calculations for isolated atoms. Features of the unique spatial and electronic environment that are directly related to the anomalous dispersion are ignored, although these can be observed spectroscopically. This significantly affects the fit between the crystallographic model and the measured intensities when the excitation wavelength in an X-ray diffraction experiment is close to an element's absorption edge. Herein, we report on synchrotron multi-wavelength single-crystal X-ray diffraction, as well as X-ray absorption spectroscopy experiments which we performed on the mol-ecular compound Mo(CO)6 at energies around the molybdenum K edge. The dispersive (f') and absorptive (f'') terms of the anomalous dispersion can be refined as independent parameters in the full-matrix least-squares refinement. This procedure has been implemented as a new feature in the well-established OLEX2 software suite. These refined parameters are in good agreement with the independently recorded X-ray absorption spectrum. The resulting crystallographic models show significant improvement compared to those employing tabulated values.
| S-EPMC9438505 | biostudies-literature
Project description:In the title coordination polymer, [Dy2(C6H8O4)(C2O4)2(H2O)2] n , the asymmetric unit consists of one Dy(3+) cation, one half of an adipate anion, two halves of oxalate anions and one coordinating water mol-ecule. The adipate and oxalate ions are located on centres of inversion. The Dy(3+) cation has a distorted tricapped trigonal-prismatic geometry and is coordinated by nine O atoms, four belonging to three adipate anions, four to two oxalate anions and one from an aqua ligand. The cations are bridged by adipate ligands, generating a two-dimensional network parallel to (010). This network is further extended into three dimensions by coordination of the rigid oxalate ligands and is further consolidated by O-H⋯O hydrogen bonds. A part of the adipate anion is disordered over two positions in a 0.75:0.25 ratio.
| S-EPMC4257430 | biostudies-literature
Project description:The title compound, [Sn(C3H7)2(H2O)(C2O4)] n , represents the first diorganotin(IV) oxalate hydrate to be structurally characterized. The tin(IV) atom of the one-dimensional coordination polymer is located on a twofold rotation axis and is coordinated by two chelating oxalate ligands with two slightly different Sn-O bond lengths of 2.290 (2) and 2.365 (2) Å, two symmetry-related n-propyl groups with a Sn-C bond lengths of 2.127 (3) Å, and a water mol-ecule with a Sn-O bond length of 2.262 (2) Å. The coordination polyhedron around the Sn(IV) atom is a slightly distorted penta-gonal bipyramid with a nearly linear axis between the trans-oriented n-propyl groups [C-Sn-C = 176.8 (1)°]. The bond angles between the oxygen atoms of the equatorial plane range from 70.48 (6)° to 76.12 (8)°. A one-dimensional coordination polymer results from the less asymmetric bilateral coordination of the centrosymmetric oxalate anion, inter-nally reflected by two slightly different C-O bond lengths of 1.248 (3) and 1.254 (3) Å. The chains of the polymer propagate parallel to [001] and are held together by hydrogen bonds between water mol-ecules and oxalate anions of neighboring chains, leading to a two-dimensional network parallel to (100).
| S-EPMC4158495 | biostudies-literature
Project description:In the title coordination polymer, {[Sr(C2H5NO2)2(H2O)3]Br2} n , the Sr(2+) ion and one of the water mol-ecules are located on twofold rotation axes. The alkaline earth ion is nine-coordinated by three water O atoms and six O atoms of the carboxyl-ate groups of four glycine ligands, two in a chelating mode and two in a monodentate mode. The glycine mol-ecule exists in a zwitterionic form and bridges the cations into chains parallel to [001]. The Br(-) counter-anions are located between the chains. Inter-molecular hydrogen bonds are formed between the amino and carboxyl-ate groups of neighbouring glycine ligands, generating a head-to-tail sequence. Adjacent head-to-tail sequences are further inter-connected by inter-molecular N-H⋯Br hydrogen-bonding inter-actions into sheets parallel to (100). O-H⋯Br and O-H⋯O hydrogen bonds involving the coordinating water mol-ecules are also present, consolidating the three-dimensional hydrogen-bonding network.
| S-EPMC4518974 | biostudies-literature
Project description:Collapsin response mediator proteins (CRMPs) are cytosolic phosphoproteins that are mainly involved in neuronal cell development. In humans, the CRMP family comprises five members. Here, crystal structures of human CRMP-4 in a truncated and a full-length version are presented. The latter was determined from two types of crystals, which were either twinned or partially disordered. The crystal disorder was coupled with translational NCS in ordered domains and manifested itself with a rather sophisticated modulation of intensities. The data were demodulated using either the two-lattice treatment of lattice-translocation effects or a novel method in which demodulation was achieved by independent scaling of several groups of intensities. This iterative protocol does not rely on any particular parameterization of the modulation coefficients, but uses the current refined structure as a reference. The best results in terms of R factors and map correlation coefficients were obtained using this new method. The determined structures of CRMP-4 are similar to those of other CRMPs. Structural comparison allowed the confirmation of known residues, as well as the identification of new residues, that are important for the homo- and hetero-oligomerization of these proteins, which are critical to nerve-cell development. The structures provide further insight into the effects of medically relevant mutations of the DPYSL-3 gene encoding CRMP-4 and the putative enzymatic activities of CRMPs.
| S-EPMC4051505 | biostudies-literature
Project description:In eukaryotes, the poly(A) tail added at the 3' end of an mRNA precursor is essential for the regulation of mRNA stability and the initiation of translation. Poly(A) polymerase (PAP) is the enzyme that catalyzes the poly(A) addition reaction. Multiple isoforms of PAP have been identified in vertebrates, which originate from gene duplication, alternative splicing or post-translational modifications. The complexity of PAP isoforms suggests that they might play different roles in the cell. Phylogenetic studies indicate that vertebrate PAPs are grouped into three clades termed α, β and γ, which originated from two gene duplication events. To date, all the available PAP structures are from the PAPα clade. Here, we present the crystal structure of the first representative of the PAPγ clade, human PAPγ bound to cordycepin triphosphate (3'dATP) and Ca(2+). The structure revealed that PAPγ closely resembles its PAPα ortholog. An analysis of residue conservation reveals a conserved catalytic binding pocket, whereas residues at the surface of the polymerase are more divergent.
| S-EPMC3878066 | biostudies-literature
Project description:In the crystal structure of the polymeric title compound, [Mn(NCS)2(C10H8N2)] n , the Mn(II) cations are coordinated by one chelating 2,2'-bi-pyridine ligand and four thio-cyanate anions (two N- and two S-coordinating), forming a distorted [MnN4S2] octa-hedron. The asymmetric unit consists of one manganese cation located on a twofold rotation axis and half of a 2,2'-bi-pyridine ligand, the other half being generated by the same twofold rotation axis, as well as one thio-cyanate anion in a general position. The Mn(II) cations are linked by two pairs of μ1,3-bridging thio-cyanate ligands into chains along the c axis; because the N atoms of the 2,2'-bi-pyridine ligands, as well as the N and the S atoms of the thio-cyanate anions, are each cis-coordinating, these chains show a zigzag arrangement.
| S-EPMC4257407 | biostudies-literature
Project description:Poly(ADP-ribose) polymerase-1 (PARP-1) has become an important pharmacological target in the treatment of cancer due to its cellular role as a 'DNA-strand break sensor', which leads in part to resistance to some existing chemo- and radiological treatments. Inhibitors have now been developed which prevent PARP-1 from synthesizing poly(ADP-ribose) in response to DNA-breaks and potentiate the cytotoxicity of DNA damaging agents. However, with the recent discoveries of PARP-2, which has a similar DNA-damage dependent catalytic activity, and additional members containing the 'PARP catalytic' signature, the isoform selectivity and resultant pharmacological effects of existing inhibitors are brought into question. We present here the crystal structure of the catalytic fragment of murine PARP-2, at 2.8 A resolution, and compare this to the catalytic fragment of PARP-1, with an emphasis on providing a possible framework for rational drug design in order to develop future isoform-specific inhibitors.
| S-EPMC373339 | biostudies-literature