The application of direct methods and Patterson interpretation to high-resolution native protein data

1993 ◽  
Vol 49 (1) ◽  
pp. 18-23 ◽  
Author(s):  
G. M. Sheldrick ◽  
Z. Dauter ◽  
K. S. Wilson ◽  
H. Hope ◽  
L. C. Sieker
Keyword(s):  
High Resolution ◽  
Direct Methods ◽  
Native Protein

scholarly journals Streamlined Methods for the Resolution and Quantification of Fatty Acids Including Trans Fatty Acid Isomers in Food Products by Gas Chromatography

2009 ◽  
Vol 92 (5) ◽  
pp. 1301-1309 ◽  
Author(s):  
Pierre-Alain Golay ◽  
Francesca Giuffrida ◽  
Fabiola Dionisi ◽  
Frédéric Destaillats
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
High Resolution ◽  
Methyl Esters ◽  
Direct Methods ◽  
Food Products ◽  
Response Factors ◽  
Geometrical Isomers ◽  
Cost Constraints ◽  
Wide Range

Abstract To support labeling, claims, and authenticity of food products, industry needs reliable methods for the analysis of fatty acids, including Trans fatty acids (TFA). In finished products, precise quantification of TFA can be problematic due to the occurrence of various positional and geometrical isomers originating from different sources, such as animal fats or processed vegetable oils and fats. The risk of underestimating TFA amounts is particularly high when inappropriate GC conditions are used. Complex sample preparation procedures involving purification of TFA isomers by silver ion chromatography have been well-documented and used for research purposes. However, in the food industry, time and cost constraints do not permit multiple analytical steps; therefore, streamlined methods are necessary. Direct methods include preparation of fatty acid methyl esters directly from food samples without prior extraction. The appropriate resolution is obtained using high-resolution GC with a highly polar 100 m capillary column, and quantification is achieved using experimentally determined response. We found that it is possible to quantify TFA in the range of 0.01 to 5.00 g/100 g of lipids in a wide range of food products. In addition, the use of direct transmethylation, response factors, and high-resolution GC allow accurate quantification of other fatty acids, including polyunsaturated and long-chain polyunsaturated fatty acids.

The Pseudo-Atom Approximation in Direct Phase Determination of Protein Structures.

1997 ◽  
Vol 3 (S2) ◽  
pp. 1025-1026
Author(s):  
Douglas L. Dorset
Keyword(s):  
Fourier Transform ◽  
High Resolution ◽  
Protein Structures ◽  
Direct Methods ◽  
Direct Solution ◽  
Phase Problem ◽  
Electron Crystallography ◽  
Phase Determination ◽  
The Fourier Transform

In principle, the availability of high-resolution micrographs in electron crystallography is a direct solution of the phase problem that has been used to great advantage for the study of proteins. However, as the resolution of the determination increases, the Fourier transform of the micrograph becomes a less accurate phase source. Hence, alternative direct methods for phase determination have been evaluated, if only to extend the resolution of most reliable lower resolution phases to the limit of the electron diffraction pattern. The first demonstration of its feasibility was published in a study of bacteriorhodopsin extending 15 Å image phases to beyond 3 Å by maximum entropy and likelihood procedures i. Later studies demonstrated that convolutional methods also can be effective.In protein crystallography, there is always an interest in carrying out a true ab initio determinations, if only because of the challenge to traditional direct methods that become statistically less reliable as the number of atoms in the unit cell increases.

Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 Å structure solution

1999 ◽  
Vol 55 (9) ◽  
pp. 1620-1622 ◽  
Author(s):  
Liu Yu-dong ◽  
I. Harvey ◽  
Gu Yuan-xin ◽  
Zheng Chao-de ◽  
He Yi-zong ◽  
...  
Keyword(s):  
Electron Density ◽  
Phase Error ◽  
Direct Methods ◽  
Anomalous Scattering ◽  
Refined Model ◽  
Native Protein ◽  
Acta Cryst ◽  
Density Maps ◽  
Structure Solution ◽  
Unknown Structure

The structure of rusticyanin is the largest unknown structure (Mr = 16.8 kDa) which has been recently solved by the direct-methods approach using only single-wavelength anomalous scattering (SAS) data from the native protein [Harvey et al. (1998). Acta Cryst. D54, 629–635]. Here, the results of the Sim distribution approach [Hendrickson & Teeter (1981). Nature (London), 290, 107–113] and of the CCP4 procedure MLPHARE [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763] are compared with those from direct methods. Analysis against the final refined model shows that direct methods produced significantly better phases (average phase error 56°) and therefore significantly better electron-density maps than the Sim distribution and MLPHARE approaches (average phase error was around 63° in both cases).

scholarly journals Solving Crystal Structures from Powder Diffraction Data

1985 ◽  
Vol 38 (3) ◽  
pp. 497 ◽  
Author(s):  
A Nørlund Christensen ◽  
MS Lehmann ◽  
M Nielsen
Keyword(s):  
High Resolution ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
Profile Data ◽  
X Ray ◽  
R Factor ◽  
Symmetric Structure ◽  
Acceptable Quality

High resolution powder data from both neutron and X-ray (synchrotron) sources have been used to estimate the possibility of direct structure determination from powder data. Two known structures were resolved by direct methods with neutron and X-ray data. With synchrotron X-ray data, the measured range of data was insufficient for a structure analysis, but the R-factor calculations showed the intensities extracted from the profile data to be of acceptable quality. The results were used to estimate the largest structure that might be solved using routine techniques. It was found that the limit would be near twenty atoms in the asymmetric part of a centro-symmetric structure.

Phase refinement of copper perchlorophthalocyanine from a 0.23 nm-resolution electron micrograph using the Sayre equation

1994 ◽  
Vol 52 ◽  
pp. 100-101
Author(s):  
Douglas L. Dorset ◽  
Sophie Kopp ◽  
John R. Fryer ◽  
William F. Tivol ◽  
James N. Turner
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Primary Source ◽  
Direct Methods ◽  
Ccd Camera ◽  
Basis Set ◽  
X Rays ◽  
Contrast Transfer Function ◽  
Lattice Images ◽  
Integrated Intensities

The use of direct methods of phasing for electron diffraction (ED) presents opportunities which cannot be matched with x-ray diffraction. High-resolution lattice images of thin crystals obtained on the electron microscope can provide crystallographic phases after image averaging and correction for the contrast transfer function--a procedure which has no analog for x-rays. This procedure has been used for protein crystallography, where such images are often the primary source for phase information.The method has also been used in the analysis of organic molecules.A high resolution (0.23 nm) electron microscope image of epitaxially oriented copper perchlorophthalocyanine obtained at 500 kV (Fig. 1) was used to provide a basis set of 39 phases for refinement in conjunction with a set of ED amplitudes obtained at 1200 kV (Fig 2). Portions of the image were digitized with a CCD camera and a frame-grabber and analyzed using the CRISP software package. The ED pattern was scanned using a Joyce-Loebl Mk. IIIC flatbed microdensitometer to produce integrated intensities, to which no Lorenz correction was applied.

Combining direct methods with isomorphous replacement or anomalous scattering data. VIII. Phasing experimental SIR data with the replacing atoms in a centrosymmetric arrangement

1999 ◽  
Vol 55 (4) ◽  
pp. 846-848 ◽  
Author(s):  
Yu-Dong Liu ◽  
Yuan-Xin Gu ◽  
Chao-De Zheng ◽  
Q. Hao ◽  
Hai-Fu Fan
Keyword(s):  
Cluster Analysis ◽  
Phase Difference ◽  
Direct Method ◽  
Direct Methods ◽  
Scattering Data ◽  
Anomalous Scattering ◽  
Phase Ambiguity ◽  
Native Protein ◽  
Figures Of Merit ◽  
Isomorphous Replacement

A multisolution direct method has been proposed to resolve the phase ambiguity intrinsic in single isomorphous replacement data of proteins with the replacing atoms in a centrosymmetric arrangement. The phase ambiguity of each reflection is in fact a `sign ambiguity' of the phase difference between the phase of the native protein and that of the replacing atoms, i.e. ± |Δφ| = φ − φ′. The P + probability formula can be used to derive the signs. The multisolution phasing procedure is initiated using random starting values of P +. A cluster analysis is used instead of figures of merit to find the correct solution. The direct-method phases can be further improved by density-modification techniques. The method was tested with the experimental SIR data at 2 Å resolution from a known protein aPP; satisfactory results were obtained.

Crystal structure of dicalcium chromate hydrate

2004 ◽  
Vol 19 (2) ◽  
pp. 133-136
Author(s):  
C. E. Botez ◽  
P. W. Stephens ◽  
Oladipo Omotoso
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Direct Methods ◽  
Rietveld Analysis ◽  
Double Layers ◽  
Powder Diffraction Data ◽  
Monoclinic Symmetry ◽  
X Ray ◽  
Symmetry Space ◽  
Symmetry Space Group

Direct methods and Rietveld analysis were applied to high-resolution synchrotron X-ray powder diffraction data to solve the crystal structure of dicalcium chromate hydrate (Ca2CrO5⋅3H2O). The compound crystallizes in monoclinic symmetry (space group Cm, Z=2), with a=8.23575(5) Å, b=7.90302(4) Å, c=5.20331(3) Å, and β=98.0137(3)°. The structure is built from double-layers of CrO4 tetrahedra and CaO8 polyhedra that run parallel to the (001) plane.

Direct space methods of structure determination from powder diffraction: principles, guidelines and perspectives

2007 ◽  
Vol 222 (3-4) ◽  
Author(s):  
Radovan Černý ◽  
Vincent Favre-Nicolin
Keyword(s):  
Global Optimization ◽  
High Resolution ◽  
Powder Diffraction ◽  
Structure Determination ◽  
Direct Methods ◽  
Complex Structures ◽  
Short History ◽  
Structure Solution ◽  
Diffraction Structure ◽  
History Of

In the last twenty five years structure determination from powder diffraction has evolved from a complex, time-consuming method to one easily usable. While the use of direct methods is restricted to samples well crystallized (sharp peaks, high resolution diffraction), structure solution using global optimization in direct space have become extremely popular, using either publicly or commercially available software. In this article we present a short history of direct space methods of structure determination from powder diffraction, and a list of available software. We then give an overview of frequent issues when solving structures in direct space, as well as how algorithms are currently evolving to solve more complex structures.

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