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Phase Set (phase + set)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Phasing possibilities using different wavelengths with a xenon derivative

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2002
Santosh Panjikar
Xenon derivatives are generally expected to be isomorphous with the native; however, the K - and L -absorption edges are not easily accessible on most synchrotron beamlines, which might limit their usefulness in phase determination. Various phasing procedures for xenon-derivatized porcine pancreatic elastase have been investigated using data sets measured at three generally accessible wavelengths. The importance of highly redundant data in measuring precise anomalous differences is highlighted and it is shown that, after such measurements, a single isomorphous replacement anomalous scattering (SIRAS) procedure yields a better phase set than those generated by single anomalous scattering (SAS) or multiwavelength anomalous diffraction (MAD) procedures. [source]

Phase determination via Sayre-type equations with anomalous-scattering data

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2001
Jeffrey Roach
The necessary background for the analysis of complex-valued electron-density maps is established. Various systems of structure-factor equations of convolutional type akin to Sayre's squaring method equations are tested for agreement on the real and imaginary parts of the electron density as well as approximations thereof. A system of convolutional structure-factor equations holding in a complex-valued electron density generated by two atom types is developed. The scope of application of these equations is determined and it is shown that the equations provide a method of extrapolating high-resolution phases from a low-resolution base phase set without introducing further model bias. Additional applications to phase refinement are explored. [source]

Determination of zinc incorporation in the Zn-substituted gallophosphate ZnULM-5 by multiple wavelength anomalous dispersion techniques

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010
M. Helliwell
The location of isomorphously substituted zinc over eight crystallographically different gallium sites has been determined in a single-crystal study of the gallophosphate ZnULM-5, GaZn(PO4)14(HPO4)2(OH)2F7, [H3N{CH2}6NH3]4, 6H2O, in an 11 wavelength experiment, using data from Station 9.8, SRS Daresbury. The measurement of datasets around the K edges of both Ga and Zn, as well as two reference datasets away from each absorption edge, was utilized to selectively exploit dispersive differences of each metal atom type in turn, which allowed the major sites of Zn incorporation to be identified as the metal 1 and 3 sites, M1 and M3. The preferential substitution of Zn at these sites probably arises because they are located in double four-ring (D4R) building units which can relax to accommodate the incorporation of hetero atoms. As the crystal is non-centrosymmetric, with space group P21212, it was also possible to use anomalous differences to corroborate the results obtained from the dispersive differences. These results were obtained firstly from difference Fourier maps, calculated using a phase set from the refined structure from data measured at the Zr K edge. Also, refined dispersive and anomalous occupancies, on an absolute scale, could be obtained using the program MLPHARE, allowing estimates for the Zn incorporation of approximately 22 and 18 at. % at the M1 and M3 sites to be obtained. In addition, f, and f,, values for Ga and Zn at each wavelength could be estimated both from MLPHARE results, and by refinement in JANA2006. The fully quantitative determinations of the dispersive and anomalous coefficients for Ga and Zn at each wavelength, as well as metal atom occupancies over the eight metal atom sites made use of the CCP4's MLPHARE program as well as SHELXL and JANA2006. The results by these methods agree closely, and JANA2006 allowed the ready determination of standard uncertainties on the occupancy parameters, which were for M1 and M3, 20.6,(3) and 17.2,(3),at %, respectively. [source]

High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5,AMP

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001
Pascal Retailleau
Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS,adenylate product (TAM) complex to a resolution limit of 1.7,Å. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS combinations with native data. Hendrickson,Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9,Å structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25,Å and from the native model by 0.38,Å, but all have r.m.s. deviations of ,1.0,Å from the 2.9,Å model. Difference Fourier calculations between amplitudes from the 300,K experiment and the new amplitudes at 100,K using 1.7,Å model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria. [source]

Solving the crystal structures of zeolites using electron diffraction data.

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2008

The maximum-entropy and likelihood method for solving zeolite crystal structures from electron diffraction data is modified to use potential-map-density histograms as an additional figure of merit. The experimental histogram is compared to an idealized one (based on known zeolite structures) using Pearson and Spearman correlation coefficients. These supplement the use of log-likelihood estimates as figures of merit to select the optimal solution from a collection of phase sets. The method has been applied with success to seven zeolite and one inorganic crystal structures that have varying associated data quality. The technique works easily even with two-dimensional data sets of less than 50 unique diffraction data and a resolution of less than 2,Å. The method is very fast, and the computer time needed on a modest PC was never more than a few minutes. [source]