Packing analysis of carbohydrates and polysaccharides. 16. The crystal structures of celluloses IVI and IVII

1985 ◽  
Vol 63 (1) ◽  
pp. 173-180 ◽  
Author(s):  
Eric S. Gardiner ◽  
Anatole Sarko
Keyword(s):  
Crystal Structures ◽  
Unit Cell ◽  
Hydroxyl Groups ◽  
Data Sets ◽  
Cell Parameters ◽  
The Difference ◽  
Cellulose Iv ◽  
Chain Conformations ◽  
Probable Space ◽  
Packing Analysis

The crystal structures of cellulose polymorphs IVI and IVII have been determined by X-ray fiber diffraction analysis combined with stereochemical model refinement. Both structures crystallize in a two-chain unit cell of essentially identical parameters. The most probable space group in both cases is P1. The chain conformations, although close to two-fold helical, are marked by unequal rotational positions of the O(6) hydroxyl groups in adjacent residues. Despite identical unit cell parameters, the structures differ in chain polarity: in cellulose IVI both chains of the unit cell are parallel, whereas in cellulose IVII they are antiparallel. The difference in polarity is further substantiated by the results of chemical conversions which show that cellulose IVI is converted to cellulose I, and cellulose IVII is converted to cellulose II, via parallel and antiparallel cellulose triacetates, respectively. The reliability of the structure analyses is indicated by the residual R″ = 0.115 for cellulose IVI and 0.094 for cellulose IVII, for data sets of 41 and 43 reflections, respectively.

Kinematical and Dynamical CBED Pattern Models: Increasing the Accuracy of the Unit-Cell Parameter Measurements Based on CBED Patterns

1990 ◽  
Vol 48 (2) ◽  
pp. 540-541
Author(s):  
I.N. Yadhikov ◽  
S.K. Maksimov
Keyword(s):  
Reciprocal Lattice ◽  
Unit Cell ◽  
Reciprocal Lattice Vector ◽  
Unit Cell Parameters ◽  
Lattice Vector ◽  
Cell Parameters ◽  
Accuracy Of Measurements ◽  
The Difference ◽  
Image Position ◽  
Convergent Beam

Convergent beam electron diffraction (CBED) is widely used as a microanalysis tool. By the relative position of HOLZ-lines (Higher Order Laue Zone) in CBED-patterns one can determine the unit cell parameters with a high accuracy up to 0.1%. For this purpose, maps of HOLZ-lines are simulated with the help of a computer so that the best matching of maps with experimental CBED-pattern should be reached. In maps, HOLZ-lines are approximated, as a rule, by straight lines. The actual HOLZ-lines, however, are different from the straights. If we decrease accelerating voltage, the difference is increased and, thus, the accuracy of the unit cell parameters determination by the method becomes lower.To improve the accuracy of measurements it is necessary to give up the HOLZ-lines substitution by the straights. According to the kinematical theory a HOLZ-line is merely a fragment of ellipse arc described by the parametric equationwith arc corresponding to change of β parameter from -90° to +90°, wherevector, h - the distance between Laue zones, g - the value of the reciprocal lattice vector, g‖ - the value of the reciprocal lattice vector projection on zero Laue zone.

scholarly journals New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations

2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee
Keyword(s):  
Crystal Structures ◽  
Adenylate Kinase ◽  
Bound States ◽  
Critical Role ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Ligand Free ◽  
Adenylate Kinases

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

Crystallization and preliminary X-ray studies of sialidase L from the leech Macrobdella decora

1998 ◽  
Vol 54 (1) ◽  
pp. 111-113 ◽  
Author(s):  
Yu Luo ◽  
Min-yuan Chou ◽  
Su-chen Li ◽  
Yu-teh Li ◽  
Ming Luo
Keyword(s):  
Escherichia Coli ◽  
Unit Cell ◽  
Data Sets ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Mercury Derivative ◽  
Macrobdella Decora

Functional monomeric 83 kDa sialidase L, a NeuAcα2→3Gal-specific sialidase from Macrobdella leech, was expressed in Escherichia coli and readily crystallized by a macroseeding technique. The crystal belongs to space group P1 with unit-cell parameters a = 46.4, b = 69.3, c = 72.5 Å, α = 113.5, β = 95.4 and γ = 107.3°. There is one molecule per unit cell, giving a Vm = 2.4 Å3 Da−1 and a solvent content of 40%. Native and mercury-derivative data sets were collected to 2.0 Å resolution. Threading and molecular-replacement calculations confirmed the existence of a bacterial sialidase-like domain.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

The structures of marialite (Me6) and meionite (Me93) in space groups P42/n and I4/m, and the absence of phase transitions in the scapolite series

2011 ◽  
Vol 26 (2) ◽  
pp. 119-125 ◽  
Author(s):  
Sytle M. Antao ◽  
Ishmael Hassan
Keyword(s):  
Phase Transitions ◽  
High Resolution ◽  
Crystal Structures ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
The Mean

The crystal structures of marialite (Me6) from Badakhshan, Afghanistan and meionite (Me93) from Mt. Vesuvius, Italy were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements. Their structures were refined in space groups I4/m and P42/n, and similar results were obtained. The Me6 sample has a formula Ca0.24Na3.37K0.24[Al3.16Si8.84O24]Cl0.84(CO3)0.15, and its unit-cell parameters are a=12.047555(7), c=7.563210(6) Å, and V=1097.751(1) Å3. The average ⟨T1-O⟩ distances are 1.599(1) Å in I4/m and 1.600(2) Å in P42/n, indicating that the T1 site contains only Si atoms. In P42/n, the average distances of ⟨T2-O⟩=1.655(2) and ⟨T3-O⟩=1.664(2) Å are distinct and are not equal to each other. However, the mean ⟨T2,3-O⟩=1.659(2) Å in P42/n and is identical to the ⟨T2′-O⟩=1.659(1) Å in I4/m. The ⟨M-O⟩ [7]=2.754(1) Å (M site is coordinated to seven framework O atoms) and M-A=2.914(1) Å; these distances are identical in both space groups. The Me93 sample has a formula of Na0.29Ca3.76[Al5.54Si6.46O24]Cl0.05(SO4)0.02(CO3)0.93, and its unit-cell parameters are a=12.19882(1), c=7.576954(8) Å, and V=1127.535(2) Å3. A similar examination of the Me93 sample also shows that both space groups give similar results; however, the C–O distance is more reasonable in P42/n than in I4/m. Refining the scapolite structure near Me0 or Me100 in I4/m forces the T2 and T3 sites (both with multiplicity 8 in P42/n) to be equivalent and form the T2′ site (with multiplicity 16 in I4/m), but ⟨T2-O⟩ is not equal to ⟨T3-O⟩ in P42/n. Using different space groups for different regions across the series implies phase transitions, which do not occur in the scapolite series.

Crystal structure of three diaza-crowns-18

1997 ◽  
Vol 212 (5) ◽  
Author(s):  
P. Dokurno ◽  
R. Trokowski ◽  
B. Kościuszko-Panek ◽  
T. Ossowski ◽  
A. Konitz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Groups ◽  
Cell Parameters

AbstractThe crystal structures of three diaza crowns-18, namely 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane (crown 1), 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diacetonitrile (crown 2) and N,N′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyldi-2,1-ethanediyl)bis-[4-methyl-benzenesulfonamide] (crown 3) have the following space groups and unit cell parameters: crown 1(C

scholarly journals Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

2010 ◽  
Vol 66 (5) ◽  
pp. 544-558 ◽  
Author(s):  
Jacco van de Streek ◽  
Marcus A. Neumann
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Density Functional ◽  
Unit Cell ◽  
Organic Crystal ◽  
Large Temperature ◽  
Unit Cell Parameters ◽  
Functional Theory ◽  
Cell Parameters ◽  
Experimental Crystal

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Structural studies of ligands for the glycine binding site of the excitatory amino acid receptor complex: 2. 6-bromo-, 6-methyl-, and 6-styryl-1,8-ethano-4-hydro-2,3-quinoxalinedione

1994 ◽  
Vol 72 (10) ◽  
pp. 2028-2036 ◽  
Author(s):  
Maciej Kubicki ◽  
Teresa W. Kindopp ◽  
Mario V. Capparelli ◽  
Penelope W. Codding
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Crystal Structures ◽  
Excitatory Amino Acid ◽  
Glycine Receptor ◽  
Three Dimensional ◽  
Unit Cell ◽  
Geometric Constraints ◽  
Cell Parameters ◽  
Π Stacking

The crystal structures of three tricyclic quinoxalinedione derivatives, 6-bromo-1,8-ethano-4-hydro-2,3-quinoxalinedione (1), 6-methyl-1,8-ethano-4-hydro-2,3-quinoxalinedione hydrate (2), and 6-styryl-1,8-ethano-4-hydro-2,3-quinoxalinedione (3), are reported. For 1 and 2, the space groups are P21/n with the unit cell parameters for 1: a = 7.4003(5) Å, b = 8.5799(5) Å, c = 14.3127(9) Å, β = 90.639(6)°, and for 2: a = 7.0590(2) Å, b = 10.7483(3) Å, c = 13.9509(7) Å, β = 103.290(3)°. For 3, the space group is P21/c, with a = 19.3683(10) Å, b = 8.0962(16) Å, c = 19.5801(16) Å, β = 114.028(6)°. Compound 3 crystallizes with two molecules in the asymmetric part of the unit cell; in one of them the styryl group is disordered. The geometries of the 1,8-ethano-4-hydro-2,3-quinoxalinedione fragments are similar in all observations, with the differences mainly caused by the different nature of the substituents in the 6-position. Hydrogen bonds connect the molecules into three-dimensional networks. Head-to-tail π-stacking between molecules connected by a center of symmetry determines the packing modes in 1 and 2 but there is no π-stacking in the crystal structure of 3. The crystal structures of the three quinoxaline derivative ligands for the glycine receptor suggest a mode of recognition that involves an [Formula: see text]receptor hydrogen bond, a three-centre hydrogen bond to the neighboring carbonyl groups on the ligand, and π-stacking between ligand and receptor. This mode is consistent with the geometric constraints of the current binding site model but places greater emphasis on hydrogen-bond interactions.

scholarly journals On the Effect of Unit-Cell Parameters in Predicting the Elastic Response of Wood-Plastic Composites

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Fatemeh Alavi ◽  
Amir Hossein Behravesh ◽  
Abbas S. Milani ◽  
Davoud Karimi
Keyword(s):  
Finite Element ◽  
Modulus Of Elasticity ◽  
Strain Curve ◽  
Unit Cell ◽  
Elastic Response ◽  
Geometrical Parameters ◽  
Uniaxial Test ◽  
Cell Parameters ◽  
Plastic Composite ◽  
The Difference

This paper presents a study on the effect of unit-cell geometrical parameters in predicting elastic properties of a typical wood plastic composite (WPC). The ultimate goal was obtaining the optimal values of representative volume element (RVE) parameters to accurately predict the mechanical behavior of the WPC. For each unit cell, defined by a given combination of the above geometrical parameters, finite element simulation in ABAQUS was carried out, and the corresponding stress-strain curve was obtained. A uniaxial test according to ASTM D638-02a type V was performed on the composite specimen. Modulus of elasticity was determined using hyperbolic tangent function, and the results were compared to the sets of finite element analyses. Main effects of RVE parameters and their interactions were demonstrated and discussed, specially regarding the inclusion of two adjacent wood particles within one unit cell of the material. Regression analysis was performed to mathematically model the RVE parameter effects and their interactions over the modulus of elasticity response. The model was finally employed in an optimization analysis to arrive at an optimal set of RVE parameters that minimizes the difference between the predicted and experimental moduli of elasticity.

scholarly journals Serial Crystallography with Multi-stage Merging oi 1000’s of Images

2017 ◽  
Author(s):  
Herbert J. Bernstein ◽  
Lawrence C. Andrews ◽  
James Foadi ◽  
Martin R. Fuchs ◽  
Jean Jakoncic ◽  
...  
Keyword(s):  
Data Clustering ◽  
Clustering Algorithms ◽  
Unit Cell ◽  
Physical Parameters ◽  
Data Sets ◽  
Cell Parameters ◽  
Cell Clustering ◽  
Multi Stage ◽  
Cluster Data ◽  
Serial Crystallography

KAMO and Blend provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options to increase the sensitivity to differences in unit cell parameters and to allow for clustering of nearly complete datasets on the basis of intensity or amplitude differences. If datasets are already sufficiently complete to permit it, apply KAMO once, just for reflections. If starting from incomplete datasets, one applies KAMO twice, first using cell parameters. In this step either the simple cell vector distance of the original Blend is used, or the more sensitive NCDist, to find clusters to merge to achieve sufficient completeness to allow intensities or amplitudes to be compared. One then uses KAMO again using the correlation between the reflections at the common HKLs to merge clusters in a way sensitive to structural differences that may not perturb the cell parameters sufficiently to make meaningful clusters.Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which can then be merged to, hopefully, yield the electron density from a single protein iso-form. What is striking about many of these physical parameters is that they are largely independent from one another. Consequently, it should be possible to greatly improve the efficacy of data clustering software by using a multi-stage partitioning strategy. Here, we have demonstrated one possible approach to multi-stage data clustering. Our strategy was to use unit-cell clustering until merged data was of sufficient completeness to then use intensity based clustering. We have demonstrated that, using this strategy, we were able to accurately cluster data sets from crystals that had subtle differences.

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