CrystalCMP: an easy-to-use tool for fast comparison of molecular packing

2016 ◽  
Vol 49 (6) ◽  
pp. 2172-2183 ◽  
Author(s):  
Jan Rohlíček ◽  
Eliška Skořepová ◽  
Martin Babor ◽  
Jan Čejka
Keyword(s):  
Molecular Packing ◽  
Unit Cell ◽  
Molecular Cluster ◽  
Data Sets ◽  
Group Setting ◽  
New Approach ◽  
Cell Parameters ◽  
Low Sensitivity ◽  
Molecular Compounds ◽  
Identical Crystal

A new approach is introduced for the comparison of molecular packing and the identification of identical crystal structure motifs. It has been tested on data sets for the solid forms of benzamide, cabergoline and trospium. In this approach, the packing similarity is calculated using a simple formula involving the distances between molecular centres and the relative orientations of molecular entities inside a finite molecular cluster. The approach is independent of the atomic labelling, the unit-cell parameters, the space group setting and the number of molecules in the asymmetric part of the unit cell. Owing to its low sensitivity to volume changes, this approach allows the comparison of various solid forms (such as polymorphs, hydrates, solvates, co-crystals or salts) of identical or similar molecular compounds. The method is also suitable for identifying similar results from direct space methods, which are often used in powder diffraction.

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.

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.

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.

The crystal structure of barikaite

2013 ◽  
Vol 77 (8) ◽  
pp. 3093-3104 ◽  
Author(s):  
E. Makovicky ◽  
D. Topa
Keyword(s):  
Lone Electron Pair ◽  
Microprobe Analysis ◽  
Electron Microprobe Analysis ◽  
Unit Cell ◽  
Double Layers ◽  
Group Setting ◽  
Cell Parameters ◽  
Lattice Setting ◽  
Cation Sites ◽  
Trigonal Prismatic

AbstractElectron microprobe analysis of barikaite (Topa et al., 2013) indicates the chemical formula Ag2.90Tl0.04Pb9.31As11.26Sb8.12S40.37. Barikaite is monoclinic, with a 8.533(1) Å, b 8.075(1) Å, c 24.828(2) Å, and β 99.077(1)°; unit-cell volume 1689.2 Å3 and the space-group setting is P21/n. This compares well with the unit-cell parameters of rathite Pb10Tl0.9As17.9Sb1.3Ag2S40 from the Lengenbach deposit with the same lattice setting. Barikaite is a member of sartorite homologous series (N = 4). The unit cell of barikaite contains eight cation sites and ten anion sites. Four of the cation sites have mixed occupancies – the split sites As2–Sb2, As3–Sb3, Ag5–As5 and the site Me6 with three cations involved. Two of the lead sites, Pb1 and Pb2, display tricapped trigonal prismatic coordinations and alternate along the 8.53 Å a direction. They form zig-zag walls parallel to (001). There are three distinct [100] columns of alternating cations, As1–(As, Sb)2, Sb4–(As, Sb)3 and (As, Ag)5–(Pb, Sb)6 which together form trapezoidally configured single (013) layers. These layers aggregate into tightly-bonded double layers, separated by lone electron pair micelles. In barikaite, the predominantly As-occupied and Sb-occupied sites are distributed in a chess-board-like scheme.

scholarly journals Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting

2014 ◽  
Vol 70 (8) ◽  
pp. 2111-2124 ◽  
Author(s):  
Christopher Farley ◽  
Geoffry Burks ◽  
Thomas Siegert ◽  
Douglas H. Juers
Keyword(s):  
Crystal Size ◽  
Ambient Air ◽  
Unit Cell ◽  
Data Sets ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Ambient Relative Humidity ◽  
Combining Data ◽  
Low Humidity ◽  
Cell Variation

In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection.

Isostructural phase transition in m-carboxyphenylammonium monohydrogenphosphite

2005 ◽  
Vol 61 (6) ◽  
pp. 700-709 ◽  
Author(s):  
El-Eulmi Bendeif ◽  
Slimane Dahaoui ◽  
Michel François ◽  
Nourredine Benali-Cherif ◽  
Claude Lecomte
Keyword(s):  
Phase Transition ◽  
Reciprocal Lattice ◽  
Forthcoming Paper ◽  
Unit Cell ◽  
Temperature Phase ◽  
Data Sets ◽  
Scanning Calorimetry ◽  
Cell Parameters ◽  
Higher Temperature ◽  
Lower Temperature

Crystals of m-carboxyphenylammonium monohydrogenphosphite, C7H8NO_{2}^+·H2PO_3^{-} (m-CPAMP), space group P2_{1}/c, grown from aqueous solution undergo a reversible first-order single-crystal phase transition at Tc = 246 (2) K with a hysteresis of 3.6 K. The thermal behaviour of the sample was characterized by differential scanning calorimetry (DSC) experiments. Variations of the unit-cell parameters versus temperature between 100 and 320 K are reported. The transition from the higher-temperature phase (HTP) to the lower-temperature phase (LTP) is characterized by a unit-cell volume contraction of 1.77%. The average structure and unit-cell packing of m-CPAMP at lower temperature (100 K) are reported from accurate X-ray data sets and compared with those of the higher-temperature phase (293 K) in order to investigate the mechanism of the phase transition. The reciprocal lattice reconstruction showed a few very weak satellite reflections which will be discussed in a forthcoming paper.

scholarly journals Phase composition of Bi2O3 specimens doped with Ti, Zr and Hf

2012 ◽  
Vol 77 (8) ◽  
pp. 1091-1096 ◽  
Author(s):  
Dejan Poleti ◽  
Ljiljana Karanovic ◽  
Miodrag Zdujic ◽  
Cedomir Jovalekic
Keyword(s):  
Crystal Structure ◽  
Phase Composition ◽  
Powder Diffraction ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Powder Mixtures ◽  
X Ray ◽  
Cell Parameters ◽  
Identical Crystal

Powder mixtures of ?-Bi2O3 containing 2, 5 and 10 mole % of TiO2, ZrO2 or HfO2 were homogenized, heated at 820?C for 24 h and quenched in air. X-ray powder diffraction technique was used to characterize the prepared samples. In all cases metastable Bi2O3 polymorphs, ?-Bi2O3 or ?-Bi2O3, are found as single or major phases. Addition of Ti4+ ions stabilizes ?-Bi2O3 polymorph, while either Zr4+ or Hf4+ ions stabilize ?-Bi2O3 polymorph. In the samples with 2 and 5 mole % of TiO2 the presence of even two ?-Bi2O3 phases (Bi12TiO20 compound and a very low Ti-doped ?-Bi2O3) was established. Similarly, in the sample with 2 mole % of HfO2 two ?-Bi2O3 phases were found. Phase composition of prepared samples, values of unit cell parameters and the appearance of two polymorphs with identical crystal structure but different unit cell parameters are discussed and compared with known data.

Twinning in 5-fluorosalicylic acid: description of a new polymorph

2018 ◽  
Vol 74 (1) ◽  
pp. 1-6
Author(s):  
Martin Lutz ◽  
Jara F. Vliem ◽  
Hendrik P. Rodenburg
Keyword(s):  
Crystal Structure ◽  
Unit Cell ◽  
Monoclinic Crystal System ◽  
Asymmetric Unit ◽  
Group Setting ◽  
Unit Cell Parameters ◽  
Monoclinic Crystal ◽  
Acta Cryst ◽  
Cell Parameters ◽  
Crystal System

The crystal structure of 5-fluorosalicylic acid is known from the literature [Choudhury & Guru Row (2004). Acta Cryst. E60, o1595–o1597] as crystallizing in the monoclinic crystal system with space-group setting P21/n and with one molecule in the asymmetric unit (polymorph I). We describe here a new polymorph which is again monoclinic but with different unit-cell parameters (polymorph II). Polymorph II has two molecules in the asymmetric unit. Its structure was modelled as a twin, with a pseudo-orthorhombic C-centred twin cell.

scholarly journals Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization

2012 ◽  
Vol 68 (7) ◽  
pp. 816-819 ◽  
Author(s):  
Benjamin Stieglitz ◽  
Katrin Rittinger ◽  
Lesley F. Haire
Keyword(s):  
Escherichia Coli ◽  
Protein Concentration ◽  
Unit Cell ◽  
Data Sets ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
One Step

An N-terminal fragment of human SHARPIN was recombinantly expressed inEscherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space groupP43212, with unit-cell parametersa = b = 61.55,c= 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively.

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