scholarly journals Initial phases from phosphate SAD in the direct methods determination of RNA

2014 ◽  
Vol 70 (a1) ◽  
pp. C612-C612
Author(s):  
Blaine Mooers ◽  
Tzanko Doukov ◽  
Tina McKay ◽  
Akila Venkataramany ◽  
Victoria Mooers
Keyword(s):  
Diffraction Data ◽  
Structure Determination ◽  
Hybrid Approach ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Anomalous Diffraction ◽  
Long Wavelength ◽  
Minimum Number ◽  
Wavelength Radiation ◽  
Phase Angles

Atomic resolution diffraction data from crystals of double-stranded RNAs can often resist automated structure determination by ab initio methods including charge flipping and traditional direct methods. Often it is possible to obtain quick success at direct methods structure determination by supplying the positions of one or more heavier atoms, which are used to calculate a starting set of phase angles. Long wavelength radiation such as that near the iron K absorption edge can be used to measure the weak anomalous diffraction data from phosphorous atoms in the RNA backbones. These anomalous diffraction data can be used to locate the positions of some of the phosphorous atoms. Next, the phosphorous positions can be used to provide initial phases for direct methods structure determination with atomic resolution diffraction data collected with shorter wavelength radiation. We tested this hybrid approach with two double-stranded RNAs, one with 31 unique phosphates and a second with 44 unique phosphates. We used a combination of programs including those in the CCP4, SHELX, and Sir program suites. We varied the number of sweeps of images collected at the iron edge to find the minimum number (and hence minimum exposure) required to find enough of the phosphate substructure for success at direct methods with the native data before collecting atomic resolution diffraction data with the short wavelength radiation. Our results suggest that diffraction data could be collected at these two wavelengths from a single crystal to avoid problems with non-isomorphism.

scholarly journals Structure determination from X-ray powder diffraction data at low resolution

2014 ◽  
Vol 70 (a1) ◽  
pp. C143-C143
Author(s):  
Hongliang Xu
Keyword(s):  
Single Crystal ◽  
Diffraction Pattern ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Powder Diffraction Data ◽  
Low Resolution

Knowledge of the structural arrangement of atoms in solids is necessary to facilitate the study of their properties. The best and most detailed structural information is obtained when the diffraction pattern of a single crystal a few tenths of a millimeter in each dimension is analyzed, but growing high-quality crystals of this size is often difficult, sometimes impossible. However, many crystallization experiments that do not yield single crystals do yield showers of randomly oriented micro-crystals that can be exposed to X-rays simultaneously to produce a powder diffraction pattern. Direct Methods routinely solve crystal structures when single-crystal diffraction data are available at atomic resolution (1.0-1.2Å), but fail to determine micro-crystal structures due to reflections overlapping and low-resolution powder diffraction data. By artificially and intelligently extending the measured data to atomic resolution, we have successfully solved structures having low-resolution diffraction data that were hard to solve by other direct-method based computation procedures. The newly developed method, Powder Shake-and-Bake, is implemented in a computer program PowSnB. PowSnB can be incorporated into the state-of-the-art software package EXPO that includes powder data reduction, structure determination and structure refinement. The new combination could have potential to solve structures that have never been solved before by direct-methods approach.

STRUCTURE DETERMINATION OF THE Ge(111)-(3×1)Ag SURFACE RECONSTRUCTION

1999 ◽  
Vol 06 (06) ◽  
pp. 1061-1065 ◽  
Author(s):  
D. GROZEA ◽  
E. BENGU ◽  
C. COLLAZO-DAVILA ◽  
L. D. MARKS
Keyword(s):  
Electron Diffraction ◽  
Surface Reconstruction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Heavy Atom ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Transmission Electron ◽  
First Time

For the first time, during the investigation of the Ag submonolayer on the Ge(111) system, large, independent domains of the Ge (111)-(3×1) Ag phase were imaged and investigated. Previous studies have reported it only as small insets between Ge (111)-(4×4) Ag and Ge (111)- c (2×8) domains. The transmission electron diffraction data were analyzed using a Direct Methods approach and "heavy-atom holography," with the result of an atomic model of the structure similar to that of Ge (111)-(3×1) Ag .

Direct methods and hypersymmetry: Structure determination of exaltone phenylsemicarbazone with low-order diffraction data

1980 ◽  
Vol 152 (3-4) ◽  
pp. 215-225 ◽  
Author(s):  
W. G. M. van den Hoek ◽  
G. Bokkers ◽  
H. Krabbendam ◽  
A. L. Spek ◽  
J. Kroon
Keyword(s):  
Diffraction Data ◽  
Structure Determination ◽  
Direct Methods ◽  
Order Diffraction ◽  
Low Order

Direct methods and simulated annealing: a hybrid approach for powder diffraction data

2008 ◽  
Vol 41 (1) ◽  
pp. 56-61 ◽  
Author(s):  
Angela Altomare ◽  
Rocco Caliandro ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Molecular Model ◽  
Hybrid Approach ◽  
Direct Methods ◽  
Heavy Atoms ◽  
The Monte Carlo Method ◽  
Structure Solution ◽  
Electron Density Map

The solution of crystal structures from powder data using direct methods can be very difficult if the quality of the diffraction pattern is low and if no heavy atoms are present in the molecule. On the contrary, the use of direct-space methods does not require good quality diffraction data, but if a molecular model is available, the structure solution is limited principally by the number of degrees of freedom used to describe the model. The combination of the information contained in the electron density map (direct methods) with the Monte Carlo method, which uses simulated annealing as a global minimization algorithm (direct-space techniques), can be a useful tool for crystal structure solution, especially for organic structures. A modified and improved version of this approach [Altomareet al.(2003),J. Appl. Cryst.36, 230–238] has been implemented in theEXPO2004program and is described here.

scholarly journals Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials

2018 ◽  
Vol 51 (5) ◽  
pp. 1262-1273 ◽  
Author(s):  
Stef Smeets ◽  
Xiaodong Zou ◽  
Wei Wan
Keyword(s):  
Electron Beam ◽  
Phase Analysis ◽  
Diffraction Data ◽  
Structure Determination ◽  
Direct Methods ◽  
Projection Algorithm ◽  
Quantitative Phase Analysis ◽  
Polycrystalline Materials ◽  
Electron Crystallography ◽  
Automated Method

Serial electron crystallography has been developed as a fully automated method to collect diffraction data on polycrystalline materials using a transmission electron microscope. This enables useful data to be collected on materials that are sensitive to the electron beam and thus difficult to measure using the conventional methods that require long exposure of the same crystal. The data collection strategy combines goniometer translation with electron beam shift, which allows the entire sample stage to be probed. At each position of the goniometer, the locations of the crystals are identified using image recognition techniques. Diffraction data are then collected on each crystal using a quasi-parallel focused beam with a predefined size (usually 300–500 nm). It is shown that with a fast and sensitive Timepix hybrid pixel area detector it is possible to collect diffraction data of up to 3500 crystals per hour. These data can be indexed using a brute-force forward-projection algorithm. Results from several test samples show that 100–200 frames are enough for structure determination using direct methods or dual-space methods. The large number of crystals examined enables quantitative phase analysis and automatic screening of materials for known and unknown phases.

scholarly journals Multi-Solution Genetic Algorithm Approach to Surface Structure Determination Using Direct Methods

1997 ◽  
Vol 53 (6) ◽  
pp. 916-922 ◽  
Author(s):  
E. Landree ◽  
C. Collazo-Davila ◽  
L. D. Marks
Keyword(s):  
Genetic Algorithm ◽  
Diffraction Data ◽  
Structure Determination ◽  
Solution Space ◽  
Direct Methods ◽  
Search Method ◽  
Surface Structures ◽  
Genetic Algorithm Approach ◽  
Surface Diffraction ◽  
Algorithm Search

We show that it is possible to use a multi-solution genetic algorithm search method utilizing direct methods to solve surface structures from surface diffraction data. We suggest that the method is generally applicable and able to replace random searches of the solution space.

Hydrothermal Preparation of Zeolite Li--A(BW), LiAlSiO4.H2O, and Structure Determination from Powder Diffraction Data by Direct Methods.

1986 ◽  
Vol 40a ◽  
pp. 500-506 ◽  
Author(s):  
P. Norby ◽  
A. Nørlund Christensen ◽  
I. G. Krogh Andersen ◽  
H. A. Hjuler ◽  
J. H. von Barner ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
Hydrothermal Preparation

Structure solution of zeolites from powder diffraction data

2004 ◽  
Vol 219 (12) ◽  
Author(s):  
Allen W. Burton
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structure Elucidation ◽  
Model Building ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
Zeolite Structure ◽  
Structure Solution

AbstractThis article reviews methods in structure determination of zeolites from powder diffraction data. First, examples of different model building techniques are discussed. Then the applications and limitations of conventional direct methods in zeolite structure solution are examined. Methods for partitioning overlapping peak intensities are also discussed, and examples are given to illustrate improvements in structure elucidation when these techniques are applied.

Applications of direct methods in protein crystallography for dealing with diffraction data down to 5 Å resolution

2014 ◽  
Vol 70 (3) ◽  
pp. 239-247 ◽  
Author(s):  
Haifu Fan ◽  
Yuanxin Gu ◽  
Yao He ◽  
Zhengjiong Lin ◽  
Jiawei Wang ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Dual Space ◽  
Heavy Atom ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Phase Problem ◽  
Phase Extension ◽  
Phase Constraints ◽  
Sad Phasing ◽  
Model Completion

Apart from solving the heavy-atom substructure in proteins andab initiophasing of protein diffraction data at atomic resolution, direct methods have also been successfully combined with other protein crystallographic methods in dealing with diffraction data far below atomic resolution, leading to significantly improved results. In this respect, direct methods provide phase constraints in reciprocal space within a dual-space iterative framework rather than solve the phase problem independently. Applications of this type of direct methods to difficult SAD phasing, model completion and low-resolution phase extension will be described in detail.

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