The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

1999 ◽  
Vol 55 (9) ◽  
pp. 1539-1545 ◽  
Author(s):  
C. F. Snook ◽  
B. A. Wallace
Keyword(s):  
Careful Consideration ◽  
Molecular Replacement ◽  
Helix Axis ◽  
Asymmetric Unit ◽  
High Resolution Data ◽  
Symmetric Structure ◽  
Structure Factors ◽  
Replacement Solution ◽  
Independent Molecules ◽  
Starting Model

The successful use of molecular-replacement methods for the solution of the intermediate-sized helical polypeptide antiamoebin I required the careful consideration of a number of parameters and exhibited some unusual characteristics when compared with molecular-replacement solutions of globular proteins. High-resolution data were required owing to several features, including the comma-like shape of the molecule (which results in a pseudo-symmetric structure at low resolution), the relative uniformity of the structure in the direction along the helix axis and the small differences between the two independent molecules in the P1 asymmetric unit. Other parameters which were important for the solution of this relatively low solvent content closely packed cell included the radius of integration, the use of normalized structure factors and especially the choice of starting model.

Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers

1999 ◽  
Vol 55 (8) ◽  
pp. 1487-1489 ◽  
Author(s):  
Chantal Abergel ◽  
Sabine Chenivesse ◽  
Marie-Georges Stinnakre ◽  
Sophie Guasco ◽  
Christian Bréchot ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Adhesion Protein ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Liver Cancers ◽  
Replacement Solution

Human HIP/PAP is an adhesion protein expressed in normal pancreatic and Paneth cells and overexpressed in hepatocellular carcinoma. HIP/PAP was crystallized using the Hampton Research Crystal Screen and SAmBA software to define the optimal crystallization protocol. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 30.73, b = 49.35, c = 92.15 Å and one molecule in the asymmetric unit. Flash-frozen crystals diffract to 1.78 Å resolution using synchrotron radiation. A molecular-replacement solution was obtained using the human Reg/lithostathine structure and the AMoRe software.

The Crystal Structure of cis-Inositol Monohydrate—Un Objet Retrouvé

1996 ◽  
Vol 49 (3) ◽  
pp. 413 ◽  
Author(s):  
HC Freeman ◽  
DA Langs ◽  
CE Nockolds ◽  
YL Oh
Keyword(s):  
Crystal Structure ◽  
Least Squares ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
High Symmetry ◽  
Asymmetric Unit ◽  
Fourier Methods ◽  
Full Matrix ◽  
Structure Factors ◽  
Independent Molecules

cis-Inositol monohydrate, C6H12O6.H2O, crystallizes in the monoclinic space group P 21/n [a 9.900(8), b 9.296(8), c 17.795(15) Ǻ, β 90.5(1)°, Z 8]. The normalized structure factors Eh have an atypical statistical distribution, and attempts to solve the structure by direct methods (triplet relationships) were unsuccessful. The structure was ultimately solved by Patterson and Fourier methods, and was refined by full-matrix least squares [Rw = 0.047 for 1665 independent reflections ≥2σ(Imin)]. The cis-inositol molecules have approximately trigonal symmetry, as expected. The difficulties encountered during the structure analysis are explained by the presence of two nearly identical molecules of high symmetry in the asymmetric unit. The independent molecules are related by translational pseudosymmetry, and their orientations are such that all the C-C and C-O bonds in the structure are approximately parallel to a small number of directions.

scholarly journals Expression, purification, crystallization and preliminary X-ray diffraction analysis of a ribokinase from the thermohalophileHalothermothrix orenii

2012 ◽  
Vol 68 (2) ◽  
pp. 240-243 ◽  
Author(s):  
Lokesh D. Kori ◽  
Andreas Hofmann ◽  
Bharat K. C. Patel
Keyword(s):  
Metal Ion ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Replacement Solution ◽  
Metal Ion Affinity Chromatography

A ribokinase gene (rbk) from the anaerobic halothermophilic bacteriumHalothermothrix oreniiwas cloned and overexpressed inEscherichia coli. The recombinant protein (Ho-Rbk) was purified using immobilized metal-ion affinity chromatography and crystals were obtained using the sitting-drop method. Diffraction data were collected to a resolution of 3.1 Å using synchrotron radiation. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 45.6,b= 61.1,c= 220.2, and contained two molecules per asymmetric unit. A molecular-replacement solution has been found and attempts are currently under way to build a model of the ribokinase. Efforts to improve crystal quality so that higher resolution data can be obtained are also being considered.

Rapid automated molecular replacement by evolutionary search

1999 ◽  
Vol 55 (2) ◽  
pp. 484-491 ◽  
Author(s):  
Charles R. Kissinger ◽  
Daniel K. Gehlhaar ◽  
David B. Fogel
Keyword(s):  
Optimization Algorithm ◽  
Search Space ◽  
Molecular Replacement ◽  
Evolutionary Search ◽  
Asymmetric Unit ◽  
Uniform Sampling ◽  
Search Models ◽  
Structure Factors ◽  
Complete Search ◽  
Multiple Molecules

A new procedure for molecular replacement is presented in which an efficient six-dimensional search is carried out using an evolutionary optimization algorithm. In this procedure, a population of initially random molecular-replacement solutions is iteratively optimized with respect to the correlation coefficient between observed and calculated structure factors. The sensitivity and reliability of the method is enhanced by uniform sampling of the rotational-search space and the use of continuously variable rotational and translational parameters. The process is several orders of magnitude faster than a systematic six-dimensional search, and comparisons show that it can identify solutions using significantly less accurate or less complete search models than is possible with two existing molecular-replacement methods. A program incorporating the method, EPMR, allows the rapid and highly automated solution of molecular-replacement problems involving single or multiple molecules in the asymmetric unit. EPMR has been used to solve a number of difficult molecular-replacement problems.

Crystallization and preliminary X-ray diffraction studies of human catalase

1999 ◽  
Vol 55 (9) ◽  
pp. 1614-1615 ◽  
Author(s):  
R. A. P. Nagem ◽  
E. A. L. Martins ◽  
V. M. Gonçalves ◽  
R. Aparício ◽  
I. Polikarpov
Keyword(s):  
Search Model ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Beef Liver ◽  
X Ray ◽  
Diffusion Technique ◽  
Cell Dimensions ◽  
Synchrotron Radiation Diffraction ◽  
Replacement Solution ◽  
Unit Cell Dimensions

The enzyme catalase (H2O2–H2O2 oxidoreductase; E.C. 11.1.6) was purified from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 Å resolution. The enzyme crystallized in the space group P212121, with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 Å. A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.

scholarly journals Crystal structure of a new monoclinic polymorph ofN-(4-methylphenyl)-3-nitropyridin-2-amine

2014 ◽  
Vol 70 (8) ◽  
pp. 58-61
Author(s):  
Aina Mardia Akhmad Aznan ◽  
Zanariah Abdullah ◽  
Vannajan Sanghiran Lee ◽  
Edward R. T. Tiekink
Keyword(s):  
Three Dimensional ◽  
Basis Set ◽  
Dihedral Angles ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Common Features ◽  
Compound C ◽  
B3lyp Level ◽  
The Common ◽  
Independent Molecules

The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, withZ′ = 4) of the previously reported monoclinic (P21/c, withZ′ = 2) form [Akhmad Aznanet al.(2010).Acta Cryst.E66, o2400]. Four independent molecules comprise the asymmetric unit, which have the common features of asyndisposition of the pyridine N atom and the toluene ring, and an intramolecular amine–nitro N—H...O hydrogen bond. The differences between molecules relate to the dihedral angles between the rings which range from 2.92 (19) to 26.24 (19)°. The geometry-optimized structure [B3LYP level of theory and 6–311 g+(d,p) basis set] has the same features except that the entire molecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C—H...O, C—H...π, nitro-N—O...π and π–π interactions [inter-centroid distances = 3.649 (2)–3.916 (2) Å].

scholarly journals 4-[(4-Bromophenyl)amino]-2-methylidene-4-oxobutanoic acid

2014 ◽  
Vol 70 (7) ◽  
pp. o779-o780
Author(s):  
B. Narayana ◽  
Prakash S. Nayak ◽  
Balladka K. Sarojini ◽  
Jerry P. Jasinski
Keyword(s):  
Hydrogen Bonds ◽  
Amide Group ◽  
Dihedral Angles ◽  
Asymmetric Unit ◽  
Carboxylic Acid Groups ◽  
Compound C ◽  
Oxobutanoic Acid ◽  
The Mean ◽  
Graph Set ◽  
Independent Molecules

In the title compound, C11H10BrNO3, two independent molecules (AandB) crystallize in the asymmetric unit. The dihedral angles between the mean planes of the 4-bromophenyl ring and amide group are 24.8 (7) in moleculeAand 77.1 (6)° in moleculeB. The mean plane of the methylidene group is further inclined by 75.6 (4) in moleculeAand 72.5 (6)° in moleculeBfrom that of the amide group. In the crystal, N—H...O hydrogen bonds formed by amide groups and O—H...O hydrogen bonds formed by carboxylic acid groups are observed and supported additionally by weak C—H...O interactions between the methylidene and amide groups. Together, these link the molecules into chains of dimers along [110] and formR22(8) graph-set motifs.

3-n-Butyl-2-methoxy-1-benzothieno[3,2-d]pyrimidin-4(3H)-one

2006 ◽  
Vol 62 (4) ◽  
pp. o1319-o1320 ◽  
Author(s):  
Min-Hui Cao ◽  
Sheng-Zhen Xu ◽  
Yang-Gen Hu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Benzene Ring ◽  
Title Compound ◽  
Thiophene Ring ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Compound C ◽  
Π Stacking ◽  
Independent Molecules

The title compound, C15H16N2O2S, contains a five-membered thiophene ring fused to a benzene ring and a substituted pyrimidinone ring. All three rings in each of the independent molecules of the asymmetric unit lie in approximately the same plane. The crystal structure is stabilized by intermolecular C—H...O hydrogen bonding and π–π stacking interactions.

Topochemically controlled solid-state methyl rearrangement in thiocyanurates

2001 ◽  
Vol 57 (3) ◽  
pp. 428-434 ◽  
Author(s):  
Mark Greenberg ◽  
Vitaly Shteiman ◽  
Menahem Kaftory
Keyword(s):  
Solid State ◽  
Driving Force ◽  
Mirror Plane ◽  
Energy Calculation ◽  
Asymmetric Unit ◽  
Methyl Transfer ◽  
Plate Shape ◽  
Polymorphic Forms ◽  
Independent Molecules ◽  
The Difference

4,6-Dimethoxy-3-methyl-1,3,5-triazine-2(3H)-thione crystallizes in two polymorphic forms, needles and plates. In the needle-shaped crystals (9a) the molecules occupy the crystallographic mirror plane, thus the layers are stacked along the b axis. The molecules of the other polymorph [plate-shape crystals, (9b)] are packed in a herringbone packing mode. Upon heating, (9b) undergoes a phase transition to form (9a). At 378 K the needles undergo O → S topochemically controlled methyl transfer in the solid state to produce 1-methyl-4-methoxy-6-methylthio-1,3,5-triazine-2(1H)-one in 75% yield. The enthalpy of the rearrangement is estimated to be −39.1 kJ mol−1. 1-Methyl-6-methoxy-4-methylthio-1,3,5-triazine-2(1H)-thione crystallizes in space group P21 with two crystallographically independent molecules in the asymmetric unit. Compound (9b) undergoes O → S methyl transfer in the solid state at 373 K. The rearrangement is topochemically assisted and the product, 1-methyl-2,4-bismethylthio-1,3,5-triazine-6(1H)-one, is obtained in quantitative yield. The enthalpy of the rearrangement is estimated to be −58.8 kJ mol−1. The crystal structures of the compounds as well as their DSC thermographs are described and discussed. Energy calculation by ab initio methods shows that the driving force for the reactions is the difference between the molecular energies of the pre-rearranged compounds and their products, 54.2 and 59.3 kJ mol−1 in the two cases, respectively.

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