J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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TL;DR: Applications and new developments of protein‐characterization methods using MS, fluorescence spectroscopy, static light scattering, analytical ultracentrifugation and small‐angle X‐ray scattering within the EC Structural Proteomics in Europe contract are described.
Abstract: Protein characterization plays a role in two key aspects of structural proteomics. The first is the quality assessment of the produced protein preparations. Obtaining well diffracting crystals is one of the major bottlenecks in the structure-determination pipeline. Often, this is caused by the poor quality of the protein preparation used for crystallization trials. Hence, it is essential to perform an extensive quality assessment of the protein preparations prior to crystallization and to use the results in the evaluation of the process. Here, a protein-production and crystallization strategy is proposed with threshold values for protein purity (95%) and monodispersity (85%) below which a further optimization of the protein-production process is strongly recommended. The second aspect is the determination of protein characteristics such as domains, oligomeric state, post-translational modifications and protein–protein and protein–ligand interactions. In this paper, applications and new developments of protein-characterization methods using MS, fluorescence spectroscopy, static light scattering, analytical ultracentrifugation and small-angle X-ray scattering within the EC Structural Proteomics in Europe contract are described. Examples of the application of the various methods are given.
76 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...In contrast, since the SLS data are based upon the scattering of light from proteins, they are independent of molecular conformation and dependent only upon the absolute molecular mass of the sample, resulting in mass determinations that are typically accurate to within 2–5%....
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TL;DR: It is shown that the combination of phase‐contrast X‐ray microtomography and high‐resolution ptychographic X-ray tomography allows the visualization and characterization of the interparticle pores at micro‐ and nanometer‐length scales.
Abstract: Porosity in catalyst particles is essential because it enables reactants to reach the active sites and it enables products to leave the catalyst. The engineering of composite-particle catalysts through the tuning of pore-size distribution and connectivity is hampered by the inability to visualize structure and porosity at critical-length scales. Herein, it is shown that the combination of phase-contrast X-ray microtomography and high-resolution ptychographic X-ray tomography allows the visualization and characterization of the interparticle pores at micro- and nanometer-length scales. Furthermore, individual components in preshaped catalyst bodies used in fluid catalytic cracking, one of the most used catalysts, could be visualized and identified. The distribution of pore sizes, as well as enclosed pores, which cannot be probed by traditional methods, such as nitrogen physisorption and isotherm analysis, were determined.
75 citations
TL;DR: In this paper, a direct real-space interpretation of G(Z) through the particle scattering density and pair correlation function is given, and the case of non-interacting particles is considered in detail with an explicit geometrical interpretation.
Abstract: Spin-echo small-angle neutron scattering (SESANS) is a novel real-space scattering technique. SESANS measures a correlation-like function G(Z), the meaning of which was unknown until now. Here a direct real-space interpretation of G(Z) through the particle scattering density and pair correlation function is given. One-dimensional and two-dimensional SESANS are compared. The case of non-interacting particles is considered in detail with an explicit geometrical interpretation. General methods for the calculation of structural parameters, such as the total scattering length and the radius of gyration, are developed. Analytical expressions of G(Z) for non-interacting solid spheres, hollow spheres and Gaussian coils are derived. The case of solid spheres is compared with experimental data.
75 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...General methods for the calculation of structural parameters, such as the total scattering length and the radius of gyration, are developed....
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...This function G(Z) depends on the spin-echo length, Z. Previous numerical calculations showed that the SESANS correlation function G(Z) is highly sensitive to the structure and size of the particles (Bouwman & Rekveldt, 2000; Uca et al., 2003)....
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TL;DR: A highly X-ray-transparent, silicon nitride-based device has been designed and fabricated to harvest protein microcrystals for high-resolution X-rays diffraction data collection using microfocus beamlines and XFELs.
Abstract: Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 A) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.
75 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...After merging, Phaser (McCoy et al., 2007) was used for molecular replacement with a polyalanine search model Acta Cryst....
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...At the Advanced Photon Source, 0.5 ml freshly prepared HEWL microcrystal slurry was pipetted onto four consecutive windows, as only four windows were accessible for data collection on each silicon nitride chip owing to the geometry of the mounting devices and beamline endstation....
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...4d)....
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...The lysozyme structure was determined by molecular replacement using Phaser (McCoy et al., 2007) and refined using phenix.refine (Adams et al., 2010), while manual rebuilding and adjustment was carried out in Coot (Emsley et al., 2010)....
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TL;DR: Examples of phasing macromolecular crystal structures based on single-wavelength anomalous dispersion (SAD) show that this approach is more powerful and may have more general application in structural biology than was anticipated.
Abstract: Examples of phasing macromolecular crystal structures based on single-wavelength anomalous dispersion (SAD) have demonstrated that this approach may have general applications in structural biology. With better data-collection facilities and cryogenic techniques, combined with powerful data-processing, phasing and density-modification programs, the SAD approach may prove simpler than phasing from multi-wavelength (MAD) measurements. It can be performed at any wavelength where anomalous scattering can be observed, in many cases using laboratory X-ray sources. However, there is still a need for accurate data, successful phase improvement and a certain amount of luck. This paper extends the discussion of Jolly SAD in Dauter et al. [Dauter, Z., Dauter, M. & Dodson, E. (2002), Acta Cryst. D58, 494–506].
75 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The wavelength used was 0.98 AÊ , where sulfur has very small values of f 0 = 0.183 and f 00 = 0.234 electrons as calculated by CROSSEC (Cromer, 1983)....
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References
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
28,425 citations
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
18,531 citations
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations