scholarly journals aCHESYM: standardized placement of macromolecular models in the unit cell

2014 ◽  
Vol 70 (a1) ◽  
pp. C336-C336
Author(s):  
Marcin Kowiel ◽  
Mariusz Jaskolski ◽  
Andrzej Gzella ◽  
Zbigniew Dauter
Keyword(s):  
Crystal Structures ◽  
Molecular Model ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Reflection Data ◽  
Interpretation Errors ◽  
Structure Solution ◽  
Asymmetric Unit Cell ◽  
Atomic Coordinates

Unique choice of the unit cell and the asymmetric unit are well defined and described in the International Tables for Crystallography vol. A. Unfortunately, the placement of molecules within the unit cell is not standardized. Since structure solution programs often use random numbers in their algorithms, the selected set of atomic coordinates may be different even with successive runs of the same program. Although formally correct, an arbitrary choice of molecular placement within the unit cell is confusing and may lead to interpretation errors [1]. With the use of the anti-Cheshire unit cell introduced by Dauter [2], for all space groups without inversion symmetry, it is possible to transform the molecular model such that its center of gravity falls within the anti-Cheshire asymmetric unit cell. It means that for macromolecular crystal structures it should be possible to standardize the placement of the molecules within the unit cell. In consequence, it should be easier for crystallographers and non-crystallographers to compare similar or related crystal structures. An implementation of the anti-Cheshire concept has been programmed in Python as a web service, aCHESYM. The aCHESYM program takes a PDB file as input and transforms the macromolecular model into the desired anti-Cheshire region. The program can also handle structure factor CIF files if the transformation used requires reindexing of the reflection data. The unit cell, coordinates and displacement parameters of all atoms after transformation are saved in a new PDB file. All the calculated transformations are reversible, so there is no danger of data loss. Moreover, the program helps the user to find the most compact assembly of the molecules (chains) in the structure when there are several chains in the asymmetric unit.

scholarly journals 4-Phenylnaphtho[2,3-c]furan-1(3H)-one, 9-Phenylnaphtho[2,3-c]furan-1(3H)-one and 3a,4-Dihydro-9-phenylnaphtho[2,3-c]furan-1(3H)-one Crystal Structures

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 857
Author(s):  
Nabyl Merbouh ◽  
Simon Cassegrain ◽  
Wen Zhou
Keyword(s):  
Crystal Structures ◽  
Unit Cell ◽  
Geometrical Parameters ◽  
Type I ◽  
Type Ii ◽  
Asymmetric Unit ◽  
Asymmetric Unit Cell

The crystal structures are reported for two unsubstituted arylnaphthalene lactones, 4-phenylnaphtho[2,3-c]furan-1(3H)-one (2), 9-phenylnaphtho[2,3-c]furan-1(3H)-one (3) and a non-aromatic dihydro arylnaphthene lactone, 3a,4-dihydro-9-phenylnaphtho[2,3-c]furan-1(3H)-one (5). There are only minor differences in the geometrical parameters of these structures. However, in certain cases, both isomers of arylnaphthalene lactones (termed Type I and Type II) were found in the same asymmetric unit cell.

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 Plasmonic terahertz detection by a double-grating-gate field-effect transistor structure with an asymmetric unit cell

2011 ◽  
Vol 99 (24) ◽  
pp. 243504 ◽  
Author(s):  
V. V. Popov ◽  
D. V. Fateev ◽  
T. Otsuji ◽  
Y. M. Meziani ◽  
D. Coquillat ◽  
...  
Keyword(s):  
Field Effect ◽  
Field Effect Transistor ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Transistor Structure ◽  
Terahertz Detection ◽  
Effect Transistor ◽  
Asymmetric Unit Cell

scholarly journals Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites

2015 ◽  
Vol 71 (9) ◽  
pp. 1161-1168 ◽  
Author(s):  
Christopher T. Jurgenson ◽  
Thomas D. Pollard
Keyword(s):  
Binding Site ◽  
Structural Information ◽  
Unit Cell ◽  
Molecular Structures ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
New Space

Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space groupP212121contained one complex per asymmetric unit, with unit-cell parametersa= 105.48,b= 156.71,c= 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space groupP41contained two complexes per asymmetric unit, with unit-cell parametersa=b= 149.93,c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small segments of subdomains 1 and 2 of Arp2. Both maps had density at the binding site on Arp3 for the C-terminal EWE tripeptide from N-WASP and a binding site proposed for the C motif of N-WASP in the barbed-end groove of Arp2. The map from the tetragonal crystal form had density near the barbed end of Arp3 that may correspond to the C helix of N-WASP. The noise levels and the low resolution of the maps made the assignment of specific molecular structures for any of these CA peptides impossible.

scholarly journals VI. Tabulated data for the examination of the 230 space-groups by homogeneous X-rays

1924 ◽  
Vol 224 (616-625) ◽  
pp. 221-257 ◽  
Keyword(s):  
Crystal Structures ◽  
Chemical Society ◽  
Unit Cell ◽  
X Rays ◽  
Screw Axis ◽  
Monoclinic System ◽  
Space Group ◽  
X Ray ◽  
Space Groups ◽  
Relative Arrangement

The object of the present paper is to express the conclusions of mathematical crystallography in a form which shall be immediately useful to workers using homogeneous X-rays for the analysis of crystal structures. The results are directly applicable to such methods as the Bragg ionisation method, the powder method, the rotating crystal method, etc., and summarise in as compact a form as possible what inferences may be made from the experimental observations, whichever one of the 230 possible space-groups may happen to be under examination. It is only in certain cases that the spacings of crystal planes as determined by the aid of homogeneous X-rays agree with the values of those spacings which would be expected from ordinary crystallographic calculations. In the majority of cases the relative arrangement of the molecules in the unit cell leads to apparent anomalies in the experimental results, the observed spacings of certain planes or sets of planes being sub-multiples of the calculated spacings. The simplest case (fig. 8) of such an apparent anomaly is found in the space-group C 2 2 of the monoclinic system, where the presence of a two-fold screw-axis, because it interleaves halfway the (010) planes by molecules which are exactly like those lying in the (010) planes, except that they have been rotated through 180°, leads to an observed periodicity which is half the periodicity to be inferred from the dimensions of the unit cell, that is, leads to an observed spacing for (010) which is half the calculated. All screw-axes produce similar results, and, in general, a p -fold screw-axis leads to an observed spacing for the plane perpendicular to it which is 1/ p th that to be inferred from the dimensions of the cell. Besides those produced by the screw-axes, other abnormalities arise out of the presence of glide-planes. The simplest case of this is shown by the space-group C s 2 (fig. 4) of the monoclinic system, in which the second molecule is obtained from the first by a reflection in a plane parallel to (010) and half a primitive translation parallel to that plane. If we look along a direction perpendicular to this glide-plane, the projections of the two molecules on the (010) plane are indistinguishable except in position, which is equivalent to saying that, for the purposes of X-ray interference, certain planes perpendicular to this plane of projection are interleaved by an identical molecular distribution. Furthermore, since the translation associated with the glide-plane must always be half a primitive translation parallel to the glide-plane, we know that the interleaving is always a submultiple of the full spacing and the periodicity is again reduced in a corresponding manner. The use of this method for discriminating between the various space-groups of the monoclinic system was described by Sir Wm. Bragg in a lecture to the Chemical Society. In the present paper the method has been extended to the whole of the 230 space-groups possible to crystalline structures. In general, it may be said that if a crystal possesses a certain glide-plane, a certain set of planes lying in the zone whose axis is perpendicular to that glide-plane will have their periodicity reduced by one-half.

Synthesis and crystal structures of two structurally related kryptoracemates

2017 ◽  
Vol 73 (7) ◽  
pp. 575-581 ◽  
Author(s):  
Philipp Kramer ◽  
Michael Bolte
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Symmetry Element ◽  
Inversion Symmetry ◽  
Asymmetric Unit ◽  
Chiral Molecules ◽  
Space Groups ◽  
Independent Molecules

Kryptoracemates are racemic compounds (pairs of enantiomers) that crystallize in Sohnke space groups (space groups that contain neither inversion centres nor mirror or glide planes nor rotoinversion axes). Thus, the two symmetry-independent molecules cannot be transformed into one another by any symmetry element present in the crystal structure. Usually, the conformation of the two enantiomers is rather similar if not identical. Sometimes, the two enantiomers are related by a pseudosymmetry element, which is often a pseudocentre of inversion, because inversion symmetry is thought to be favourable for crystal packing. We obtained crystals of two kryptoracemates of two very similar compounds differing in just one residue, namely rac-N-[(1S,2R,3S)-2-methyl-3-(5-methylfuran-2-yl)-1-phenyl-3-(pivalamido)propyl]benzamide, C27H32N2O3, (I), and rac-N-[(1S,2S,3R)-2-methyl-3-(5-methylfuran-2-yl)-1-phenyl-3-(propionamido)propyl]benzamide dichloromethane hemisolvate, C25H28N2O3·0.5CH2Cl2, (II). The crystals of both compounds contain both enantiomers of these chiral molecules. However, since the space groups [P212121 for (I) and P1 for (II)] contain neither inversion centres nor mirror or glide planes nor rotoinversion axes, there are both enantiomers in the asymmetric unit, which is a rather uncommon phenomenon. In addition, it is remarkable that (II) contains two pairs of enantiomers in the asymmetric unit. In the crystal, molecules are connected by intermolecular N—H...O hydrogen bonds to form chains or layered structures.

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