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SAD phasing by OASIS at different resolutions down to 0.30nm and below
SAD phasing by OASIS at different resolutions down to 0.30 nm and below

Yao De-Qiang,Li He,Chen Qiang,Gu Yuan-Xin,Zheng Chao-De,Lin Zheng-Jiong,Fan Hai-Fu,Nobuhisa Watanabe,Sha Bing-Dong,
姚德强
,李鹤,陈强,古元新,郑朝德,林政炯,范海福,渡邉信久,沙炳东

中国物理 B , 2008,
Abstract: Single-wavelength anomalous diffraction (SAD) phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-K\alpha source at 0.18nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40nm resolutions were used in the test. TT0570 Cu-K$\alpha$ sulfur-SAD data have an expected Bijvoet ratio <\vert\Delta F\vert>/\ \sim 0.55%. In the 0.21nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.
SAD phasing by OASIS at different resolutions down to 0.30nm and below

Yao De-Qiang,

物理学报 , 2008,
Abstract: Single-wavelength anomalous diffraction (SAD) phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-K\alpha source at 0.18nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40nm resolutions were used in the test. TT0570 Cu-K$\alpha$ sulfur-SAD data have an expected Bijvoet ratio <\vert\Delta F\vert>/\ \sim 0.55%. In the 0.21nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.
Ce-SAD Phasing of Glucose Isomerase and Thermolysin Using Cu Radiation  [PDF]
Sibi Narayanan, Devadasan Velmurugan
Crystal Structure Theory and Applications (CSTA) , 2013, DOI: 10.4236/csta.2013.23013
Abstract:

Current structural genomics projects aim to solve a large number of selected protein structures as fast as possible. High degree of automation and standardization is required at every step of the whole process to speed up protein structure determination. Phase problem is a bottleneck in macromolecular structure determination and also in model building which is a time-consuming task. The simplest approach to phasing macromolecular crystal structures is the use of a SAD signal. SAD data can be collected using the in-house copper (1.54 A) wavelength source. Data collected using copper wavelength with the incorporation of anomalously scattering heavy metal atoms may serve as a powerful tool for structural biologists to solve novel protein structures as well where synchrotron beam line is not available. A short soak of protein crystals in heavy metal solution or by incorporating heavy atoms into the protein drop while crystallizing the protein (co-crystallization) leads to incorporation of these heavy metal ions into the ordered solvent shell around the protein surface. The present work aims to determine whether cerium ion can be successfully incorporated into the protein crystal through quick-soaking method while maintaining the isomorphism. The study also aims in understanding whether this metal ion can be used for phasing purpose. The intensity data are collected and analyzed for anomalous signal, substructure solution and the binding sites.

New expression of bimodal phase distributions in direct-method phasing of protein single-wavelength anomalous diffraction data
OASIS4.0—a new version of the program OASIS for phasing protein diffraction data

Zhang Tao,Gu Yuan-Xin,Zheng Chao-De,Fan Hai-Fu,
张涛
,古元新,郑朝德,范海福

中国物理 B , 2010,
Abstract: The program OASIS4.0 has been released. Apart from the improved single-wavelength anomalous diffraction (SAD) phasing algorithm described in a separate paper, an important new feature in this version is the automation of the iterative phasing and model-building process in solving protein structures. A new graphical user's interface (GUI) is provided for controlling and real-time monitoring the dual-space iterative process. The GUI is discussed in detail in the present paper.
Direct Phasing of Nanocrystal Diffraction  [PDF]
Veit Elser
Physics , 2013,
Abstract: Recent experiments at free-electron laser x-ray sources have been able to resolve the intensity distributions about Bragg peaks in nanocrystals of large biomolecules. Information derived from small shifts in the peak positions augment the Bragg samples of the particle intensity with samples of its gradients. Working on the assumption that the nanocrystal is entirely generated by lattice translations of a particle, we develop an algorithm that reconstructs the particle from intensities and intensity gradients. Unlike traditional direct phasing methods that require very high resolution data in order to exploit sparsity of the electron density, our method imposes no constraints on the contrast other than positivity and works well at low resolution. We demonstrate successful reconstructions with simulated P1 lysozyme nanocrystal data down to a signal-to-noise ratio of 2 in the intensity gradients.
Phasing spaces of matroids  [PDF]
Emanuele Delucchi,Elia Saini
Mathematics , 2015,
Abstract: We study the space of phasing classes of phased matroids over a fixed matroid M. We generalize methods of Gel'fand, Rybnikov and Stone and we obtain three different characterizations: one of combinatorial flavor, via projective phasings (in terms of the circuits and cocircuits of M), one algebraic, as a certain subspace of the Pontrjagin dual of the inner Tutte group of M, and one geometrical as a subspace of the torus $(S^1)^N$. As applications, we provide an effectively computable formula for the rank of the inner Tutte group, we give an upper bound on the number of reorientation classes of oriented matroids on M, we prove the existence of non-realizable, non-chirotopal uniform phased matroids in any rank and we show that the complements of complex hyperplane arrangements with the same uniform matroid are diffeomorphic.
Diagnostic criterion for crystallized beams  [PDF]
Harel Primack,Reinhold Blümel
Physics , 1998, DOI: 10.1103/PhysRevE.58.6578
Abstract: Small ion crystals in a Paul trap are stable even in the absence of laser cooling. Based on this theoretically and experimentally well-established fact we propose the following diagnostic criterion for establishing the presence of a crystallized beam: Absence of heating following the shut-down of all cooling devices. The validity of the criterion is checked with the help of detailed numerical simulations.
Synchrotron radiation of crystallized beams  [PDF]
Harel Primack,Reinhold Blümel
Physics , 1998, DOI: 10.1103/PhysRevE.60.957
Abstract: We study the modifications of synchrotron radiation of charges in a storage ring as they are cooled. The pair correlation lengths between the charges are manifest in the synchrotron radiation and coherence effects exist for wavelengths longer than the coherence lengths between the charges. Therefore the synchrotron radiation can be used as a diagnostic tool to determine the state (gas, liquid, crystal) of the charged plasma in the storage ring. We show also that the total power of the synchrotron radiation is enormously reduced for crystallized beams. This opens the possibility of accelerating particles to ultra-relativistic energies using small-sized cyclic accelerators.
SAD effects on grantsmanship  [PDF]
George A. Lozano
Physics , 2014,
Abstract: Seasonal affective disorder (SAD) is a state of depression induced by a lack of sufficient sunlight that occurs at high latitudes during the fall and winter. One effect of SAD is that causes people to be more risk-adverse, an effect that should be considered by granting agencies of high latitude countries. Funding agencies often have programmes aimed at high-risk, innovative research. However, the time of the year during which these purposefully high-risk proposals are evaluated usually does not take into consideration the effects of SAD. In high-latitude countries (e.g., Canada, UK, Nordic and Baltic countries), evaluating proposals for high-risk programmes during the late fall might significantly detract from the very purpose of such programmes. At this time of the year, grant evaluators might be in a darkness-induced state of mild depression. As such, evaluators might be more likely to opt for safe investments, more of the same, the well established, which is the antithesis of innovative research.
Fourier phasing with phase-uncertain mask  [PDF]
Albert Fannjiang,Wenjing Liao
Physics , 2012, DOI: 10.1088/0266-5611/29/12/125001
Abstract: Fourier phasing is the problem of retrieving Fourier phase information from Fourier intensity data. The standard Fourier phase retrieval (without a mask) is known to have many solutions which cause the standard phasing algorithms to stagnate and produce wrong or inaccurate solutions. In this paper Fourier phase retrieval is carried out with the introduction of a randomly fabricated mask in measurement and reconstruction. Highly probable uniqueness of solution, up to a global phase, was previously proved with exact knowledge of the mask. Here the uniqueness result is extended to the case where only rough information about the mask's phases is assumed. The exponential probability bound for uniqueness is given in terms of the uncertainty-to-diversity ratio (UDR) of the unknown mask. New phasing algorithms alternating between the object update and the mask update are systematically tested and demonstrated to have the capability of recovering both the object and the mask (within the object support) simultaneously, consistent with the uniqueness result. Phasing with a phase-uncertain mask is shown to be robust with respect to the correlation in the mask as well as the Gaussian and Poisson noises.
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