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Structure Solution (structure + solution)
Kinds of Structure Solution Selected AbstractsStructure solution of the new titanate Li4Ti8Ni3O21 using precession electron diffractionACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010Mauro Gemmi A sample having stoichiometry Li[Ti1.5Ni0.5]O4 has been synthesized to obtain a spinel structure. The resulting crystalline powder revealed a multiphase nature with spinel as the minor phase. The main phase is a new trigonal phase having a = 5.05910,(1), c = 32.5371,(1),Å. The structure has been solved by direct methods working on a three-dimensional set of intensities obtained from a precession electron-diffraction experiment, and refined on synchrotron powder diffraction data in the space group . The model consists of hexagonal layers of edge-sharing octahedra occupied either by the heavy cations Ti and Ni, or preferentially by Li. On the basis of cation-site occupancies the stoichiometry becomes Li4Ti8Ni3O21, which is compatible with the microanalysis results. [source] Structure solution of the basic decagonal Al,Co,Ni phase by the atomic surfaces modelling methodACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2002Antonio Cervellino The atomic surfaces modelling technique has been used to solve the structure of the basic Ni-rich Al,Co,Ni decagonal phase. Formula Al70.6Co6.7Ni22.7, space group , five-dimensional unit-cell parameters: d1 = d4 = 4.752,(3),Å, d2 = d3 = 3.360,(2),Å, d5 = 8.1710,(2),Å; ,12 = ,34 = 69.295°, ,13 = ,24 = 45°, ,14 = 41.410°, ,23 = ,i5 = 90° (i = 1,4), V = 291.2,(7),Å5; Dx = 3.887,Mg,m,3. Refinement based on |F|; 2767 unique reflections (|F| > 0), 749 parameters, R = 0.17, wR = 0.06. Describing the structure of quasicrystals embedded in n -dimensional superspace in principle takes advantage of n -dimensional periodicity to select the minimal set of degrees of freedom for the structure. The method of modelling of the atomic surfaces yielded the first fully detailed structure solution of this phase. Comparison with numerous former, less accurate models confirms several features already derived, but adds a new essential insight of the structure and its complexity. The atoms fill the space forming recurrent structure motifs, which we will (generically) refer to as clusters. However, no unique cluster exists, although differences are small. Each cluster shows a high degree of structural disorder. This gives rise to a large configurational entropy, as much as expected in a phase which is stable at high temperature. On the other side, the cluster spatial arrangement is perfectly quasiperiodic. These considerations, corroborated by analysis of the structural relationship with neighbouring periodic phases, strongly suggest the existence of a non-local, long-range interaction term in the total energy which may be essential to the stability. [source] Away from the edge II: in-house Se-SAS phasing with chromium radiationACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2005Hao Xu Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr,K, radiation to take advantage of the larger anomalous scattering signal from selenium ( = 2.28 e,) compared with sulfur ( = 1.14 e,). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr,K, radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr,K, wavelength. A single data set to 2.2,Å resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9,h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography. [source] Crystallization and preliminary X-ray diffraction analysis of human seminal plasma protein PSP94ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Mukesh Kumar The human seminal plasma protein PSP94 is a small protein of 94 residues that contains ten cysteines. Since its discovery about 25,years ago, several potential biological functions have been reported for this protein. Many PSP94 homologues have also been identified since then from various species, but no crystal structure has been determined to date. PSP94 has been purified from human seminal plasma and crystallized. These crystals diffracted to ,2.3,Å resolution and belonged to space group P41212, with unit-cell parameters a = 107.9, b = 107.9, c = 92.1,Å. There are four molecules in the asymmetric unit. Structure solution by the heavy-atom method is currently in progress. [source] Crystallization and preliminary X-ray analysis of the complex between a Bacillus subtilis,/,-type small acid-soluble spore protein and DNAACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2007Daniela Bumbaca An engineered variant of an ,/,-type small acid-soluble spore protein (SASP) from Bacillus subtilis was crystallized in a complex with a ten-base-pair double-stranded DNA by the hanging-drop vapor-diffusion method using ammonium sulfate as a precipitating agent. Crystals grew at 281,K using sodium cacodylate buffer pH 5.5 and these crystals diffracted X-rays to beyond 2.4,Å resolution using synchrotron radiation. The crystallized complex contains two or three SASP molecules bound to one DNA molecule. The crystals belong to the hexagonal space group P6122 or P6522, with unit-cell parameters a = b = 87.0, c = 145.4,Å, , = , = 90.0, , = 120.0°. Diffraction data were 96.6% complete to 2.4,Å resolution, with an Rsym of 8.5%. Structure solution by the multiwavelength/single-wavelength anomalous dispersion method using isomorphous crystals of selenomethionine-labeled protein is in progress. [source] Solid-State Structures and Properties of Europium and Samarium HydridesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2010Holger Kohlmann Abstract The structural chemistry of europium and samarium hydrides in the solid state is very rich, ranging from typical ionic hydrides following the hydride-fluoride analogy to complex transition metal hydrides and interstitial hydrides. While crystal structure, electrical, and magnetic properties suggest that europium is divalent in all hydrides investigated so far, samarium is easily transformed to a trivalent oxidation state in its hydrides and shows similarities to other lanthanide(III) hydrides. The problem of neutron absorption of europium and samarium, hampering crystal structure solution and limiting the available structural information, is discussed in detail, and practical solutions for neutron diffraction experiments are given. [source] Ba6Si6N10O2(CN2) , A Nitridosilicate with a NPO-Zeolite Structure Type Containing Carbodiimide IonsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2009Sandro Pagano Abstract A new precursor approach leading to NPO-zeolite analogous nitridosilicates with cavities containing carbodiimide ions is presented. The reaction of amorphous "Si(CN2)2" and barium in liquid sodium afforded Ba6Si6N10O2(CN2) as yellow crystals. The structure is a rare example of the NPO-zeolite framework type and the first nitridosilicate incorporating carbodiimide ions. The partially ordered integration of carbodiimide moieties in the channels leads to the formation of a superstructure (P, no. 174, a = 16.255(2), c = 5.4690(11) Å, Z = 3, R1 = 0.0299, 2139 data, 100 parameters) and merohedral twinning. A comprehensive structure solution is presented, taking all possible ordering variants and twin laws into account.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Structures of Four Crystal Forms of DecaplaninHELVETICA CHIMICA ACTA, Issue 5 2003Christopher Lehmann The glycopeptide antibiotic decaplanin (1; formerly known as MM 47761 and M86-1410) crystallizes in two P21 and two P6122 crystal forms, each with four monomers in the asymmetric unit, with solvent contents varying from 48 to 69%. Although with ca. 600 unique atoms, the structures are larger than typical small molecules, one was solved by direct methods. The other three were solved by typical macromolecular methods: single-wavelength anomalous diffraction (SAD) of the Cl-atoms present naturally in the structure, multiple-wavelength anomalous diffraction (MAD) at the Br absorption edge for a crystal soaked in NaBr solution, and molecular replacement. There is evidence of appreciable radiation damage with loss of 20,30% of the covalent and ionic halogens affecting the synchrotron datasets that may even have unintentionally facilitated the MAD structure solution. The structures contain the dimer units typical of antibiotics related to vancomycin, but, in addition, there are a variety of further intermolecular interactions responsible for the polymorphy leading to intertwined 61 -helices in two of the crystal forms. Except for the sugars and some sidechains, the conformations of the 16 independent monomers are very similar. [source] Teaching crystallography to undergraduate physical chemistry studentsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5-2 2010Virginia B. Pett Teaching goals, laboratory experiments and homework assignments are described for teaching crystallography as part of two undergraduate physical chemistry courses. A two-week teaching module is suggested for introductory physical chemistry, including six to eight classroom sessions, several laboratory experiences and a 3,h computer-based session, to acquaint undergraduate physical chemistry students with crystals, diffraction patterns, the mathematics of structure determination by X-ray diffraction, data collection, structure solution and the chemical insights available from crystal structure information. Student projects and laboratory work for three to four weeks of an advanced physical chemistry course are presented. Topics such as symmetry operators, space groups, systematic extinctions, methods of solving the phase problem, the Patterson map, anomalous scattering, synchrotron radiation, crystallographic refinement, hydrogen bonding and neutron diffraction all lead to the goal of understanding and evaluating a crystallographic journal article. Many of the ideas presented here could also be adapted for inorganic chemistry courses. [source] PSSP, a computer program for the crystal structure solution of molecular materials from X-ray powder diffraction dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2010Silvina Pagola This work describes the computer program PSSP (powder structure solution program) for the crystal structure solution of molecular solids from X-ray powder diffraction data. This direct-space structure solution program uses the simulated annealing global optimization algorithm to minimize the difference between integrated intensities calculated from trial models and those extracted in a Le Bail fit of the experimental pattern, using a cost function for dealing with peak overlap through defined intensity correlation coefficients, computationally faster to calculate than Rwp. The methodology outlined is applicable to organic solids composed of moderately complex rigid and flexible molecules, using diffraction data up to relatively low resolution. PSSP performance tests using 11 molecular solids with six to 20 degrees of freedom are analyzed. [source] Ab initio structure solution by iterative phase-retrieval methods: performance tests on charge flipping and low-density eliminationJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2010Frank Fleischer Comprehensive tests on the density-modification methods charge flipping [Oszlányi & Süt, (2004). Acta Cryst. A60, 134,141] and low-density elimination [Shiono & Woolfson (1992). Acta Cryst. A48, 451,456] for solving crystal structures are performed on simulated diffraction data of periodic structures and quasicrystals. A novel model-independent figure of merit, which characterizes the reliability of the retrieved phase of each reflection, is introduced and tested. The results of the performance tests show that the quality of the phase retrieval highly depends on the presence or absence of an inversion center and on the algorithm used for solving the structure. Charge flipping has a higher success rate for solving structures, while low-density elimination leads to a higher accuracy in phase retrieval. The best results can be obtained by combining the two methods, i.e. by solving a structure with charge flipping followed by a few cycles of low-density elimination. It is shown that these additional cycles dramatically improve the phases not only of the weak reflections but also of the strong ones. The results can be improved further by averaging the results of several runs and by applying a correction term that compensates for a reduction of the structure-factor amplitudes by averaging of inconsistently observed reflections. It is further shown that in most cases the retrieved phases converge to the best solution obtainable with a given method. [source] An approach for eliminating chemically unreasonable structure models with overlapping atoms as implemented within the GEST softwareJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2010Zhen Jie Feng A close-contact penalty factor has been added to the GEST structure solution from powder diffraction data software to differentiate chemically unreasonable structure models from potentially correct models. In order to eliminate the chemically unreasonable structures, the penalty factor is added to the Bragg R factor. This has proved to be an effective approach. [source] EXPO2009: structure solution by powder data in direct and reciprocal spaceJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2009Angela Altomare The program EXPO2009 is the evolution of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025,1028]. EXPO2009 performs all the steps of ab initio structure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced in EXPO2009 for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compounds, when traditional approaches like direct methods may fail. The EXPO2009 graphical interface has been optimized and made very user friendly. [source] ReX: a computer program for structural analysis using powder diffraction dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2009Mauro Bortolotti Multi-platform software has been developed for the analysis of powder diffraction data, with particular focus on structure solution. The program provides a Rietveld optimization engine, with the possibility of refining parameters describing both the sample and the instrument model. Geometric constraints such as rigid fragments and torsion angles can be defined for the atomic structure, to reduce the number of degrees of freedom of the model. An innovative hierarchical description of the asymmetric unit has been adopted, which allows, in principle, the definition of arbitrarily complex geometric relationships. Additionally, global optimization algorithms may be used in place of the standard nonlinear least squares, when particularly challenging problems are being faced. [source] Symmetry determination following structure solution in P1JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2008L. Palatinus A new method for space-group determination is described. It is based on a symmetry analysis of the structure-factor phases resulting from a structure solution in space group P1. The output of the symmetry analysis is a list of all symmetry operations compatible with the lattice. Each symmetry operation is assigned a symmetry agreement factor that is used to select the symmetry operations that are the elements of the space group of the structure. On the basis of the list of the selected operations the complete space group of the structure is constructed. The method is independent of the number of dimensions, and can also be used in solution of aperiodic structures. A number of cases are described where this method is particularly advantageous compared with the traditional symmetry analysis. [source] The revenge of the Patterson methods.JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2007In the present paper, the third and last of a series (the first two papers were dedicated to the crystal structure solution of proteins), the Patterson superposition method, based on the use of the symmetry minimum function, has been applied to powder diffraction patterns. The method has been modified to take into account the special challenges of this kind of data and to optimize the performance of the approach. The new algorithms have been implemented in a computer program and applied also to single-crystal data of small and medium-size crystal structures. The experimental results have been compared with those obtained via direct methods, so enabling the role and the perspectives of these two approaches in the global phasing problem to be established, no matter what the experimental technique (powder or single-crystal diffraction) or the size of the structures (small, medium or macro-molecules). [source] The revenge of the Patterson methods.JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2007The Patterson techniques, recently developed by the same authors for the ab initio crystal structure solution of proteins, have been applied to single and multiple anomalous diffraction (SAD and MAD) data to find the substructure of the anomalous scatterers. An automatic procedure has been applied to a large set of test structures, some of which were originally solved with remarkable difficulty. In all cases, the procedure automatically leads to interpretable electron density maps. Patterson techniques have been compared with direct methods; the former seem to be more efficient than the latter, so confirming the results obtained for ab initio phasing, and disproving the common belief that they could only be applied to determine large equal-atom substructures with difficulty. [source] The combined use of Patterson and Monte Carlo methods for the decomposition of a powder diffraction patternJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2006Angela Altomare The success of ab initio crystal structure solution by powder diffraction data is strictly related to the quality of the integrated intensity estimates. A new method that is able to improve the pattern decomposition step has been developed. It combines the inversion of a suitably modified Patterson map with the use of the Hamming codes [13,10] and [40,36] in order to explore more decomposition trials. The new approach has been introduced in EXPO2005, an updated version of EXPO2004, and successfully applied to a set of known organic and inorganic structures. [source] Structure determination of diclofenac in a diclofenac-containing chitosan matrix using conventional X-ray powder diffraction dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2004Nongnuj Muangsin The structure determination of diclofenac embedded in a diclofenac-containing chitosan matrix using conventional X-ray powder diffraction data is demonstrated. It reveals that sodium diclofenac, the starting material in the preparation of a controlled-release diclofenac-containing chitosan matrix, changes to diclofenac acid in space group C2/c in the matrix. Simple methods were employed for handling the sample to obtain X-ray powder diffraction data of sufficiently high quality for the determination of the crystal structure of diclofenac embedded in chitosan. These involved grinding and sieving several times through a micro-mesh sieve to obtain a suitable particle size and a uniformly spherical particle shape. A traditional technique for structure solution from X-ray powder diffraction data was applied. The X-ray diffraction intensities were extracted using Le Bail's method. The structure was solved by direct methods from the extracted powder data and refined using the Rietveld method. For comparison, the single-crystal structure of the same drug was also determined. The result shows that the crystal structure solved from conventional X-ray powder diffraction data is in good agreement with that of the single crystal. The deviations of the differences in bond lengths and angles are of the order of 0.030,Å and 0.639°, respectively. [source] The application of structure envelopes in structure determination from powder diffraction dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2002Simon Brenner A structure envelope is a special type of periodic nodal surface that separates regions of high electron density from those of low electron density. Once such a surface has been generated, it can be used in combination with direct-space methods to facilitate structure solution from powder data. To generate an informative structure envelope, the phases of the structure factors of a few strong low-order reflections must be determined; an algorithm has been developed for this purpose. The program SayPerm combines (a) the use of error-correcting codes (e.c.c.'s) to sample phase space efficiently, (b) a pseudo-atom approximation of structure fragments to simulate atomic resolution at ca 2.5,Å, and (c) phase extension and phase set ranking using the Sayre equation. The effect of using a structure envelope in structure solution was first tested in combination with a subroutine for finding zeolite topologies in the program FOCUS. Then extension to molecular structures in combination with a simulated-annealing program was explored. This resulted in the development of the program Safe and the subsequent determination of the structure of a tri-,-peptide (C32N3O6H53) with 17 variable torsion angles. [source] Solving crystal structures in P1: an automated procedure for finding an allowed origin in the correct space groupJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2000Maria Cristina Burla Crystal structure solution in P1 may be particularly suitable for complex crystal structures crystallizing in other space groups. However, additional efforts and human intervention are often necessary to locate correctly the structural model so obtained with respect to an allowed origin of the actual space group. An automatic procedure is described which is able to perform such a task, allowing the routine passage to the correct space group and the subsequent structure refinement. Some tests are presented proving the effectiveness of the procedure. [source] Towards an understanding of radiation damage in cryocooled macromolecular crystalsJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2005Colin Nave Interest in radiation damage is growing rapidly owing to the surge in macromolecular crystallography experiments carried out at modern brilliant synchrotron macromolecular crystallography beamlines. Work on the characterization of radiation damage in cryocooled protein crystals is starting to have some impact on our understanding of the problem and of how damage might be affecting both the process of structure solution and the actual structure obtained. A brief review of the most recent developments is given together with an assessment of the remaining problems. Although progress is being made, the understanding of radiation damage is far from complete. Methods for recognizing the damage and treating the data are being made available but they are still at an early stage of development. [source] Applications of ACORN to data at 1.45 Å resolutionJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004V. Rajakannan One of the main interests in the molecular biosciences is in understanding structure,function relations and X-ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The , helices and , sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 Å (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 Å resolution and also to truncated data at 1.6 Å resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for `seed-phasing' to ACORN. [source] Diffusion-equation method for crystallographic figure of meritsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2010Anders J. Markvardsen Global optimization methods play a significant role in crystallography, particularly in structure solution from powder diffraction data. This paper presents the mathematical foundations for a diffusion-equation-based optimization method. The diffusion equation is best known for describing how heat propagates in matter. However, it has also attracted considerable attention as the basis for global optimization of a multimodal function [Piela et al. (1989). J. Phys. Chem.93, 3339,3346]. The method relies heavily on available analytical solutions for the diffusion equation. Here it is shown that such solutions can be obtained for two important crystallographic figure-of-merit (FOM) functions that fully account for space-group symmetry and allow the diffusion-equation solution to vary depending on whether atomic coordinates are fixed or not. The resulting expression is computationally efficient, taking the same order of floating-point operations to evaluate as the starting FOM function measured in terms of the number of atoms in the asymmetric unit. This opens the possibility of implementing diffusion-equation methods for crystallographic global optimization algorithms such as structure determination from powder diffraction data. [source] Comparative refinement of correct and incorrect structural models of tetrabutylammonium tetrabutylborate , pitfalls arising from poor-quality dataACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2010Vladimir Stilinovi This paper demonstrates how numerical parameters usually used to assess the quality of a crystal structure solution (R, wR and S) may be misleading when studying a model refined against poor-quality data. Weakly diffracting crystals of tetrabutylammonium tetrabutylborate, a low-density organic salt comprising isoelectronic cations and anions, were measured using Cu and Mo K, radiation. Along with the correct structural model, six erroneous structural models were constructed and refined against the same data. For both data sets it was found that models based on an incorrect unit-cell choice give lower values of R and wR than the correct one, thus apparently being in better agreement with measured data. Closer inspection of the measured data shows that this is in fact not the case. [source] The difference electron density: a probabilistic reformulationACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2010Maria Cristina Burla The joint probability distribution function P(E, Ep), where E and Ep are the normalized structure factors of the target and of a model structure, respectively, is a fundamental tool in crystallographic methods devoted to crystal structure solution. It plays a central role in any attempt for improving phase estimates from a given structure model. More recently the difference electron density ,q = ,,,p has been revisited and methods based on its modifications have started to play an important role in combination with electron density modification approaches. In this paper new coefficients for the difference electron density have been obtained by using the joint probability distribution function P(E, Ep, Eq) and by taking into account both errors in the model and in measurements. The first applications show the correctness of our theoretical approach and the superiority of the new difference Fourier synthesis, particularly when the model is a rough approximation of the target structure. The new and the classic difference syntheses coincide when the model represents the target structure well. [source] Structure determination without Fourier inversion.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009The parameter-space concept for solving crystal structures from reflection amplitudes (without employing or searching for their phases) is described on a theoretically oriented basis. Emphasis is placed on the principles of the method, on selecting one of three types of parameter spaces discussed in this paper, and in particular on the structure model employed (equal-atom point model, however usually reduced to one-dimensional projections) and on the system of `isosurfaces' representing experimental `geometrical structure amplitudes' in an orthonormal parameter space of as many dimensions as unknown atomic coordinates. The symmetry of the parameter space as well as of the imprinted isosurfaces and its effect on solution methods is discussed. For point atoms scattering with different phases or signs (as is possible in the case of X-ray resonant or of neutron scattering) it is demonstrated that the `landscape' of these isosurfaces remains invariant save certain shifts of origin known beforehand (under the condition that all atomic scattering amplitudes have been reduced to 1 thus meeting the requirement of the structure model above). Partly referring to earlier publications on the subject, measures are briefly described which permit circumventing an analytical solution of the system of structure-amplitude equations and lead to either a unique (unequivocal) approximate structure solution (offering rather high spatial resolution) or to all possible solutions permitted by the experimental data used (thus including also all potential `false minima'). A simple connection to Patterson vectors is given, also a first hint on data errors. References are given for practical details of various solution techniques already tested and for reconstruction of three-dimensional structures from their projections by `point tomography'. We would feel foolish if we tried to aim at any kind of `competition' to existing methods. Having mentioned `pros and cons' of our concept, some ideas about potential applications are nevertheless offered which are mainly based on its inherent resolution power though demanding rather few reflection data (use of optimal intensity contrast included) and possibly providing a result proven to be unique. [source] A synergistic approach to protein crystallization: Combination of a fixed-arm carrier with surface entropy reductionPROTEIN SCIENCE, Issue 5 2010Andrea F. Moon Abstract Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier-driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail. [source] Symmetry-modified charge flippingACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2009Alexander Eggeman The charge-flipping algorithm has been adapted to allow symmetry constraints to be included during the solution of structures from diffraction data. Rather than impose symmetry at the start of the algorithm, which is known to cause the process to stagnate, it is shown that the algorithm must be allowed to find an intermediate stable solution first. Although care is needed when using this modified algorithm, the improvement in the fidelity of the structure solution is considerable. [source] Automated technologies and novel techniques to accelerate protein crystallography for structural genomicsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2008Babu A. Manjasetty Dr. Abstract The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis. [source] | |||||||||||||||||||||||||