scholarly journals Rapid cadmium SAD phasing at the standard wavelength (1 Å)

2017 ◽  
Vol 73 (7) ◽  
pp. 581-590 ◽  
Author(s):  
Saravanan Panneerselvam ◽  
Esa-Pekka Kumpula ◽  
Inari Kursula ◽  
Anja Burkhardt ◽  
Alke Meents
Keyword(s):  
Crystal Growth ◽  
Data Set ◽  
Cadmium Ions ◽  
Experimental Phasing ◽  
Wide Range ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Single Data ◽  
Nucleotide Binding Proteins ◽  
Cation Complexes

Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP–divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e.no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing.

scholarly journals Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

2015 ◽  
Vol 71 (12) ◽  
pp. 2519-2525 ◽  
Author(s):  
Takanori Nakane ◽  
Changyong Song ◽  
Mamoru Suzuki ◽  
Eriko Nango ◽  
Jun Kobayashi ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Crystal Structures ◽  
Structure Determination ◽  
Anomalous Diffraction ◽  
Native Sulfur ◽  
Wide Range ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.

scholarly journals Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing

2016 ◽  
Vol 72 (3) ◽  
pp. 346-358 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Gábor Bunkóczi ◽  
Li-Wei Hung ◽  
Peter H. Zwart ◽  
Janet L. Smith ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Atomic Displacement ◽  
Peak Height ◽  
High Ratio ◽  
Data Set ◽  
High Data ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Displacement Factor ◽  
Difference Fourier

A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. A simple theoretical framework for describing measurements of anomalous differences and the resulting useful anomalous correlation and anomalous signal in a SAD experiment is presented. Here, the useful anomalous correlation is defined as the correlation of anomalous differences with ideal anomalous differences from the anomalous substructure. The useful anomalous correlation reflects the accuracy of the data and the absence of minor sites. The useful anomalous correlation also reflects the information available for estimating crystallographic phases once the substructure has been determined. In contrast, the anomalous signal (the peak height in a model-phased anomalous difference Fourier at the coordinates of atoms in the anomalous substructure) reflects the information available about each site in the substructure and is related to the ability to find the substructure. A theoretical analysis shows that the expected value of the anomalous signal is the product of the useful anomalous correlation, the square root of the ratio of the number of unique reflections in the data set to the number of sites in the substructure, and a function that decreases with increasing values of the atomic displacement factor for the atoms in the substructure. This means that the ability to find the substructure in a SAD experiment is increased by high data quality and by a high ratio of reflections to sites in the substructure, and is decreased by high atomic displacement factors for the substructure.

Utilizing guanine-coordinated Zn2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

2019 ◽  
Vol 75 (1) ◽  
pp. 32-40 ◽  
Author(s):  
Caixia Hou ◽  
Oleg V. Tsodikov
Keyword(s):  
Nucleic Acids ◽  
Crystal Structures ◽  
Structural Changes ◽  
Dna Oligomers ◽  
Anomalous Diffraction ◽  
Double Stranded Dna ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Anomalous Signal

The experimental phase determination of crystal structures of nucleic acids and nucleic acid–ligand complexes would benefit from a facile method. Even for double-stranded DNA, software-generated models are generally insufficiently accurate to serve as molecular replacement search models, necessitating experimental phasing. Here, it is demonstrated that Zn2+ ions coordinated to the N7 atom of guanine bases generate sufficient anomalous signal for single-wavelength anomalous diffraction (SAD) phasing of DNA crystal structures. Using zinc SAD, three crystal structures of double-stranded DNA oligomers, 5′-AGGGATCCCT-3′, 5′-GGGATCCC-3′ and 5′-GAGGCCTC-3′, were determined. By determining the crystal structure of one of these oligomers, GAGGCCTC, in the presence of Mg2+ instead of Zn2+, it was demonstrated that Zn2+ is not structurally perturbing. These structures allowed the analysis of structural changes in the DNA on the binding of analogues of the natural product mithramycin to two of these oligomers, AGGGATCCCT and GAGGCCTC. Zinc SAD may become a routine approach for determining the crystal structures of nucleic acids and their complexes with small molecules.

scholarly journals Long-wavelength Mesh&Collect native SAD phasing from microcrystals

2019 ◽  
Vol 75 (2) ◽  
pp. 192-199 ◽  
Author(s):  
Michele Cianci ◽  
Max Nanao ◽  
Thomas R. Schneider
Keyword(s):  
Radiation Sensitivity ◽  
Time Frame ◽  
Data Sets ◽  
Data Set ◽  
Experimental Planning ◽  
Manual Intervention ◽  
Partial Data ◽  
Small Crystals ◽  
Anomalous Signal ◽  
Single Data

Harnessing the anomalous signal from macromolecular crystals with volumes of less than 10 000 µm3 for native phasing requires careful experimental planning. The type of anomalous scatterers that are naturally present in the sample, such as sulfur, phosphorus and calcium, will dictate the beam energy required and determine the level of radiation sensitivity, while the crystal size will dictate the beam size and the sample-mounting technique, in turn indicating the specifications of a suitable beamline. On the EMBL beamline P13 at PETRA III, Mesh&Collect data collection from concanavalin A microcrystals with linear dimensions of ∼20 µm or less using an accordingly sized microbeam at a wavelength of 1.892 Å (6.551 keV, close to the Mn edge at 6.549 keV) increases the expected Bijvoet ratio to 2.1% from an expected 0.7% at 12.6 keV (Se K edge), thus allowing experimental phase determination using the anomalous signal from naturally present Mn2+ and Ca2+ ions. Dozens of crystals were harvested and flash-cryocooled in micro-meshes, rapidly screened for diffraction (less than a minute per loop) and then used for serial Mesh&Collect collection of about 298 partial data sets (10° of crystal rotation per sample). The partial data sets were integrated and scaled. A genetic algorithm for combining partial data sets was used to select those to be merged into a single data set. This final data set showed high completeness, high multiplicity and sufficient anomalous signal to locate the anomalous scatterers, and provided phasing information which allowed complete auto-tracing of the polypeptide chain. To allow the complete experiment to run in less than 2 h, a practically acceptable time frame, the diffractometer and detector had to run together with limited manual intervention. The combination of several cutting-edge components allowed accurate anomalous signal to be measured from small crystals.

scholarly journals Long-wavelength native-SAD phasing: opportunities and challenges

IUCrJ ◽  
2019 ◽  
Vol 6 (3) ◽  
pp. 373-386 ◽  
Author(s):  
Shibom Basu ◽  
Vincent Olieric ◽  
Filip Leonarski ◽  
Naohiro Matsugaki ◽  
Yoshiaki Kawano ◽  
...  
Keyword(s):  
Anomalous Scattering ◽  
X Rays ◽  
X Ray ◽  
Long Wavelength ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Scattering Factor ◽  
X Ray Absorption

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

scholarly journals Choosing and Using Statistical Sources in Criminology: What Can the Crime Survey for England and Wales Tell Us?

2016 ◽  
Vol 16 (2) ◽  
pp. 78-90 ◽  
Author(s):  
Nick Tilley ◽  
Andromachi Tseloni
Keyword(s):  
British Journal ◽  
Administrative Data ◽  
Data Sets ◽  
Data Set ◽  
England And Wales ◽  
Valuable Data ◽  
Criminological Research ◽  
Wide Range ◽  
Single Data

AbstractThere is a wide range of sources that might fruitfully be used in criminological research. This article, by Andromachi Tseloni* and Nick Tilley**, overviews the type of evidence used in research that has recently appeared in the British Journal of Criminology, gives examples of unobtrusive administrative data that have been used in recent projects, and focuses on a single data set, the Crime Survey for England and Wales, which covers a wide range of criminological topics. Finally, it will be suggested that criminologists may be missing opportunities to draw on valuable data sets that, though imperfect, could be useful to them in their research.

scholarly journals Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

2016 ◽  
Vol 72 (3) ◽  
pp. 359-374 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Gábor Bunkóczi ◽  
Li-Wei Hung ◽  
Peter H. Zwart ◽  
Janet L. Smith ◽  
...  
Keyword(s):  
Figure Of Merit ◽  
Signal To Noise Ratio ◽  
Theoretical Framework ◽  
Data Sets ◽  
Signal To Noise ◽  
Acta Cryst ◽  
Data Set ◽  
Local Scaling ◽  
Sad Phasing ◽  
Anomalous Signal

A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilligeret al.(2016),Acta Cryst.D72, 346–358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. Thephenix.plan_sad_experimenttool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. Thephenix.scale_and_mergetool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and thephenix.anomalous_signaltool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing.

Customer-Related Social Stressors

2015 ◽  
Vol 14 (4) ◽  
pp. 165-181 ◽  
Author(s):  
Sarah Dudenhöffer ◽  
Christian Dormann
Keyword(s):  
Service Providers ◽  
Principal Component ◽  
Well Being ◽  
Emotional Dissonance ◽  
Social Stressors ◽  
Data Set ◽  
Confirmatory Factor Analyses ◽  
Confirmatory Factor ◽  
Service Jobs ◽  
Single Data

Abstract. The purpose of this study was to replicate the dimensions of the customer-related social stressors (CSS) concept across service jobs, to investigate their consequences for service providers’ well-being, and to examine emotional dissonance as mediator. Data of 20 studies comprising of different service jobs (N = 4,199) were integrated into a single data set and meta-analyzed. Confirmatory factor analyses and explorative principal component analysis confirmed four CSS scales: disproportionate expectations, verbal aggression, ambiguous expectations, disliked customers. These CSS scales were associated with burnout and job satisfaction. Most of the effects were partially mediated by emotional dissonance. Further analyses revealed that differences among jobs exist with regard to the factor solution. However, associations between CSS and outcomes are mainly invariant across service jobs.

Structure Guided Molecular Docking Assisted Alignment Dependent 3DQSAR Study on Steroidal Aromatase Inhibitors (SAIs) as Anti-breast Cancer Agents

2019 ◽  
Vol 16 (7) ◽  
pp. 808-817 ◽  
Author(s):  
Laxmi Banjare ◽  
Sant Kumar Verma ◽  
Akhlesh Kumar Jain ◽  
Suresh Thareja
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Aromatase Inhibitors ◽  
Direct Synthesis ◽  
3D Qsar ◽  
Chemotherapeutic Agents ◽  
Modeling Tools ◽  
Data Set ◽  
Wide Range ◽  
Steroidal Aromatase Inhibitors

Background: In spite of the availability of various treatment approaches including surgery, radiotherapy, and hormonal therapy, the steroidal aromatase inhibitors (SAIs) play a significant role as chemotherapeutic agents for the treatment of estrogen-dependent breast cancer with the benefit of reduced risk of recurrence. However, due to greater toxicity and side effects associated with currently available anti-breast cancer agents, there is emergent requirement to develop target-specific AIs with safer anti-breast cancer profile. Methods: It is challenging task to design target-specific and less toxic SAIs, though the molecular modeling tools viz. molecular docking simulations and QSAR have been continuing for more than two decades for the fast and efficient designing of novel, selective, potent and safe molecules against various biological targets to fight the number of dreaded diseases/disorders. In order to design novel and selective SAIs, structure guided molecular docking assisted alignment dependent 3D-QSAR studies was performed on a data set comprises of 22 molecules bearing steroidal scaffold with wide range of aromatase inhibitory activity. Results: 3D-QSAR model developed using molecular weighted (MW) extent alignment approach showed good statistical quality and predictive ability when compared to model developed using moments of inertia (MI) alignment approach. Conclusion: The explored binding interactions and generated pharmacophoric features (steric and electrostatic) of steroidal molecules could be exploited for further design, direct synthesis and development of new potential safer SAIs, that can be effective to reduce the mortality and morbidity associated with breast cancer.

Integrative Data Analysis from a Unifying Research Synthesis Perspective

2018 ◽  
Author(s):  
Eun-Young Mun ◽  
Anne E. Ray
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Research Synthesis ◽  
Alcohol Intervention ◽  
Data Set ◽  
Integrative Data Analysis ◽  
Level Data ◽  
Model Complex ◽  
Wide Range ◽  
Individual Participant

Integrative data analysis (IDA) is a promising new approach in psychological research and has been well received in the field of alcohol research. This chapter provides a larger unifying research synthesis framework for IDA. Major advantages of IDA of individual participant-level data include better and more flexible ways to examine subgroups, model complex relationships, deal with methodological and clinical heterogeneity, and examine infrequently occurring behaviors. However, between-study heterogeneity in measures, designs, and samples and systematic study-level missing data are significant barriers to IDA and, more broadly, to large-scale research synthesis. Based on the authors’ experience working on the Project INTEGRATE data set, which combined individual participant-level data from 24 independent college brief alcohol intervention studies, it is also recognized that IDA investigations require a wide range of expertise and considerable resources and that some minimum standards for reporting IDA studies may be needed to improve transparency and quality of evidence.

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