scholarly journals Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals

1992 ◽  
Vol 25 (3) ◽  
pp. 325-377 ◽  
Author(s):  
Martin Billeter
Keyword(s):  
Single Crystals ◽  
Protein Structures ◽  
Three Dimensional ◽  
Data Bank ◽  
Detailed Knowledge ◽  
X Ray Diffraction ◽  
Homologous Proteins ◽  
X Ray ◽  
Structural Details ◽  
Almost All

Following the first determinations of protein structures in the late 1950s and the early 1960s (see for example Kendrewet al.1960; Perutz, 1964), the three-dimensional structures of several hundred proteins have been elucidated by X-ray diffraction on single crystals. By the end of 1991, approximately 150 entries of proteins with substantially different sequences and a well resolved structure (Hobohmet al.1992) were deposited in the Protein Data Bank (Bernsteinet al.1977; Abolaet al.1987). In addition, many structures of homologous proteins or of mutants have been described, bringing the total number of entries to about 600. While it was soon accepted that almost all of these structures do indeed give a correct picture of the fold of the active protein in spite of the non-physiological environment of single crystals, it is not clear to what extent structural details are reliably described by these structures. In particular the surface of a protein may be modified due to the dense packing of protein molecules in the crystal lattice. A detailed knowledge of the protein surface is, however, essential for the understanding of the function of the protein.

Ferromagnetic Ordering in the Thallide EuPdTl2

2006 ◽  
Vol 61 (2) ◽  
pp. 159-163 ◽  
Author(s):  
Rainer Kraft ◽  
Sudhindra Rayaprol ◽  
C. Peter Sebastian ◽  
Rainer Pöttgen
Keyword(s):  
Curie Temperature ◽  
Single Crystals ◽  
Magnetic Moment ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Zintl Phase ◽  
X Ray ◽  
Divalent Europium ◽  
Ferromagnetic Ordering

AbstractThe new thallide EuPdTl2, synthesized from the elements in a sealed tantalum tube in a highfrequency furnace, was investigated by X-ray diffraction on powders and single crystals: MgCuAl2 type, Cmcm, Z = 4, a = 446.6(1), b = 1076.7(2), c = 812.0(2) pm, wR2 = 0.0632, 336 F2 values, 16 variables. The structure can be considered as an orthorhombically distorted, palladium-filled variant of the binary Zintl phase EuTl2. The palladium and thallium atoms build up a three-dimensional [PdTl2] polyanion with significant Pd-Tl (286 - 287 pm) and Tl-Tl (323 - 329 pm) interactions. The europium atoms fill distorted hexagonal channels of the [PdTl2] polyanion. Susceptibility measurements show a magnetic moment of 7.46(5) μB/Eu atom, indicative of divalent europium. EuPdTl2 is a soft ferromagnet with a Curie temperature of TC = 12.5(5) K.

Growth and structural and physical properties of diisopropylammonium bromide molecular single crystals

2016 ◽  
Vol 49 (6) ◽  
pp. 2053-2062 ◽  
Author(s):  
Harsh Yadav ◽  
Nidhi Sinha ◽  
Sahil Goel ◽  
Abid Hussain ◽  
Binay Kumar
Keyword(s):  
Single Crystals ◽  
Grown Crystal ◽  
Three Dimensional ◽  
Solution Technique ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dielectric Constant And Loss ◽  
Vis Spectroscopy ◽  
Direct Band ◽  
Crystallographic Axes

Large single crystals of the promising molecular organic ferroelectric diisopropylammonium bromide (DIPAB) have been grown by the solution technique. A structural study was performed using single-crystal X-ray diffraction analysis. The twin element of a selected DIPAB crystal was identified by a morphological study. Intermolecular interactions present in the grown crystal were explored by Hirshfeld surface (three-dimensional) and fingerprint plot (two-dimensional) studies. In UV–vis spectroscopy, the DIPAB crystal has shown high transparency with a wide direct band gap of 5.65 eV. In the photoluminescence spectrum, sharp UV and blue emissions were observed at 370, 392, 417 and 432 nm. The electrical properties were investigated by measuring the dielectric constant (∊) and loss (tanδ) of the grown crystal. The DIPAB crystal exhibits a promising piezoelectric charge coefficient (d33) value of 18 pC N−1, which makes it suitable for transducer applications. A high ferroelectric Curie temperature (Tc≃ 425 K) with high remnant polarization (20.52 µC cm−2) and high coercive field (12.25 kV cm−1) were observed in the as-grown crystal. Vickers microhardness analysis shows that the value of Meyer's index (n= 7.27) belongs to the soft material range, which was also confirmed by void analysis along three crystallographic axes. It is shown that the DIPAB crystal has potential for optical, ferroelectric and piezoelectric applications.

The Stannides EuPdSn and EuPtSn

1996 ◽  
Vol 51 (6) ◽  
pp. 806-810 ◽  
Author(s):  
Rainer Pöttgen
Keyword(s):  
Single Crystal ◽  
Single Crystals ◽  
Crystal Chemistry ◽  
Three Dimensional ◽  
Type Structure ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray

Abstract EuPdSn and EuPtSn were prepared from the elements in tantalum tubes at 1070 K and investigated by X-ray diffraction on both powder as well as single crystals. They crystallize with the TiNiSi type structure of space group Pnma and with Z = 4 formula units per cell. Both structures were refined from single-crystal diffractometer data: a = 751.24(9), b = 469.15(6), c = 804.31(9) pm, V = 0.2835(1) nm3 for EuPdSn, and a = 753.38(7), b = 467.72(4), c = 793.08(7) pm, V = 0.2795(1) nnr for EuPtSn. The structures consist of three-dimensional [PdSn] and [PtSn] polyanionic networks in which the europium atoms are embedded. The crystal chemistry of these stannides is briefly discussed

scholarly journals Synthesis, crystal structure and charge-distribution validation of a new alluaudite-type phosphate, Na2.22Mn0.87In1.68(PO4)3

2020 ◽  
Vol 76 (8) ◽  
pp. 1369-1372
Author(s):  
Abdessalem Badri ◽  
Inmaculada Alvarez-Serrano ◽  
María Luisa López ◽  
Mongi Ben Amara
Keyword(s):  
Crystal Structure ◽  
Single Crystals ◽  
Three Dimensional ◽  
Structure Type ◽  
X Ray Diffraction ◽  
Flux Method ◽  
X Ray ◽  
Coordination Numbers ◽  
Dimensional Network ◽  
Anionic Framework

Na2.22Mn0.87In1.68(PO4)3, sodium manganese indium tris(phosphate) (2.22/0.87/1.68), was obtained in the form of single crystals by a flux method and was structurally characterized by single-crystal X-ray diffraction. The compound belongs to the alluaudite structure type (space group C2/c) with general formula X(2)X(1)M(1)M(2)2(PO4)3. The X(2) and X(1) sites are partially occupied by sodium [occupancy 0.7676 (17) and 1/2] while the M(1) and M(2) sites are fully occupied within a mixed distribution of sodium/manganese(II) and manganese(II)/indium, respectively. The three-dimensional anionic framework is built up on the basis of M(2)2O10 dimers that share opposite edges with M(1)O6 octahedra, thus forming infinite chains extending parallel to [10\overline{1}]. The linkage between these chains is ensured by PO4 tetrahedra through common vertices. The three-dimensional network thus constructed delimits two types of hexagonal channels, resulting from the catenation of M(2)2O10 dimers, M(1)O6 octahedra and PO4 tetrahedra through edge- and corner-sharing. The channels are occupied by Na+ cations with coordination numbers of seven and eight.

scholarly journals MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models

2018 ◽  
Vol 74 (7) ◽  
pp. 606-620 ◽  
Author(s):  
Jouko J. Virtanen ◽  
Yang Zhang
Keyword(s):  
Protein Structures ◽  
Target Position ◽  
Protein Crystal ◽  
Conformational Search ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Homologous Proteins ◽  
X Ray ◽  
Replica Exchange Monte Carlo ◽  
Protein Models

Molecular replacement (MR) has commonly been employed to derive the phase information in protein crystal X-ray diffraction, but its success rate decreases rapidly when the search model is dissimilar to the target. MR-REX has been developed to perform an MR search by replica-exchange Monte Carlo simulations, which enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization. MR-REX was tested on a set of 1303 protein structures of different accuracies and successfully placed 699 structures at positions that have an r.m.s.d. of below 2 Å to the target position, which is 10% higher than was obtained by Phaser. However, cases studies show that many of the models for which Phaser failed and MR-REX succeeded can be solved by Phaser by pruning them and using nondefault parameters. The factors effecting success and the parts of the methodology which lead to success are studied. The results demonstrate a new avenue for molecular replacement which outperforms (and has results that are complementary to) the state-of-the-art MR methods, in particular for distantly homologous proteins.

scholarly journals Three-dimensional electron diffraction for porous crystalline materials: structural determination and beyond

2021 ◽  
Author(s):  
Zhehao Huang ◽  
Tom Willhammar ◽  
Xiaodong Zou
Keyword(s):  
Electron Diffraction ◽  
Three Dimensional ◽  
Structural Determination ◽  
New Materials ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
Crystalline Materials ◽  
X Ray ◽  
Structural Details

Three-dimensional electron diffraction is a powerful tool for accurate structure determination of zeolite, MOF, and COF crystals that are too small for X-ray diffraction. By revealing the structural details, the properties of the materials can be understood, and new materials and applications can be designed.

Ternary Indides LnRhIn2 (Ln = La, Ce, Pr, Nd, Sm) with MgCuAl2 Type Structure

2002 ◽  
Vol 57 (7) ◽  
pp. 798-802 ◽  
Author(s):  
Vasyl’ I Zaremba ◽  
Vitaliy P Dubenskiy ◽  
Rainer Pöttgena
Keyword(s):  
Single Crystals ◽  
Three Dimensional ◽  
Argon Atmosphere ◽  
Type Structure ◽  
Subsequent Annealing ◽  
X Ray Diffraction ◽  
Interatomic Distances ◽  
X Ray ◽  
Arc Melting ◽  
Trigonal Prisms

The ternary indides LnRhIn2 (Ln = La, Ce, Pr, Nd, Sm) were synthesized by arc-melting of the elements under an argon atmosphere and subsequent annealing at 870 K. The samples have been investigated by X-ray diffraction on powders and single crystals: MgCuAl2 type, Cmcm, a = 448.2(1), b = 1025.7(1), c = 795.1(1) pm, wR2 = 0.0372, 228 F2 values, 16 variables for LaRhIn2, a = 446.0(1), b = 1017.3(2), c = 792.7(1) pm for CeRhIn2, a = 444.03(6), b = 1013.1(1), c = 792.5(1) pm for PrRhIn2, a = 442.49(5), b = 1012.7(1), c = 789.3(1) pm for NdRhIn2, and a = 438.1(1), b = 1009.3(1), c = 788.3(1) pm, wR2= 0.0414, 304 F2 values, 16 variables for SmRhIn2. Geometrical motifs of these structures are tricapped trigonal prisms around the rhodium atoms. The shortest interatomic distances were observed for the Rh-In contacts: 280-282 pm for LaRhIn2 and 276-279 pm for SmRhIn2. Together, the rhodium and indium atoms build a three-dimensional [RhIn2] polyanion in which the lanthanoid atoms fill distorted pentagonal channels. According to one short La-Rh (282 pm) and Sm-Rh (284 pm) distance one can assume strong bonding of the lanthanoid atoms to the polyanion.

Single-crystal x-ray diffraction structures of covalent organic frameworks

Science ◽  
2018 ◽  
Vol 361 (6397) ◽  
pp. 48-52 ◽  
Author(s):  
Tianqiong Ma ◽  
Eugene A. Kapustin ◽  
Shawn X. Yin ◽  
Lin Liang ◽  
Zhengyang Zhou ◽  
...  
Keyword(s):  
Single Crystal ◽  
Single Crystals ◽  
Diffraction Data ◽  
General Procedure ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Covalent Organic Frameworks ◽  
X Ray Diffraction ◽  
X Ray

The crystallization problem is an outstanding challenge in the chemistry of porous covalent organic frameworks (COFs). Their structural characterization has been limited to modeling and solutions based on powder x-ray or electron diffraction data. Single crystals of COFs amenable to x-ray diffraction characterization have not been reported. Here, we developed a general procedure to grow large single crystals of three-dimensional imine-based COFs (COF-300, hydrated form of COF-300, COF-303, LZU-79, and LZU-111). The high quality of the crystals allowed collection of single-crystal x-ray diffraction data of up to 0.83-angstrom resolution, leading to unambiguous solution and precise anisotropic refinement. Characteristics such as degree of interpenetration, arrangement of water guests, the reversed imine connectivity, linker disorder, and uncommon topology were deciphered with atomic precision—aspects impossible to determine without single crystals.

Solid State Syntheses and Structure of LaPdCd2 and PrNi0.951(4)Cd2

2007 ◽  
Vol 62 (4) ◽  
pp. 610-612 ◽  
Author(s):  
Ahmet Doğan ◽  
Ute Ch. Rodewald ◽  
Rainer Pöttgen
Keyword(s):  
Rare Earth ◽  
Solid State ◽  
Single Crystals ◽  
Induction Furnace ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cadmium Compounds ◽  
Hexagonal Diamond ◽  
The Rare Earth

The intermetallic cadmium compounds LaPdCd2 and PrNi0.951(4)Cd2 were synthesized from the elements in sealed tantalum tubes in an induction furnace. Both phases were investigated by X-ray diffraction on powders and single crystals: MgCuAl2-type, Cmcm, Z = 4, a = 431.9(1), b = 1015.7(4), c = 835.7(2) pm, wR2 = 0.0436, 326 F2 values, 16 variables for LaPdCd2 and a = 420.26(8), b = 981.0(2), c = 815.3(1) pm, wR2 = 0.0404, 604 F2 values, 17 variables for PrNi0.951(4)Cd2. A small nickel deficit was observed for the PrNi0.951(4)Cd2 crystal. The cadmium atoms build up orthorhombically distorted three-dimensional networks (Cd-Cd distances: 302 - 334 pm) that resemble the structure of hexagonal diamond, lonsdaleite. Together with the palladium (nickel) atoms, [PdCd2] and [Ni0.951(4)Cd2] networks are formed which leave distorted hexagonal channels for the rare earth atoms.

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