Journal of Applied Crystallography

Published by International Union of Crystallography
Online ISSN: 1600-5767
Publications
Article
A combination of high-resolution X-ray diffractometry, Rutherford back scattering spectroscopy and secondary-ion mass spectrometry (SIMS) methods were used to characterize structural transformations of the damaged layer in Si(001) substrates heavily doped by Zn ions after a multistage thermal treatment. The shape of the SIMS profiles for Zn atoms correlates with the crystal structure of the damaged layer and depends on the presence of the following factors influencing the mobility of Zn atoms: (i) an amorphous/crystalline (a/c) interface, (ii) end-of-range defects, which are located slightly deeper than the a/c interface; (iii) a surface area enriched by Si vacancies; and (iv) the chemical interaction of Zn with Si atoms, which leads to the formation of Zn-containing phases in the surface layer.
 
Article
Vertically aligned InAs nanowires (NWs) doped with Si were grown self-assisted by molecular beam epitaxy on GaAs[111]B substrates covered with a thin SiO x layer. Using out-of-plane X-ray diffraction, the influence of Si supply on the growth process and nanostructure formation was studied. It was found that the number of parasitic crystallites grown between the NWs increases with increasing Si flux. In addition, the formation of a Ga0.2In0.8As alloy was observed if the growth was performed on samples covered by a defective oxide layer. This alloy formation is observed within the crystallites and not within the nanowires. The Ga concentration is determined from the lattice mismatch of the crystallites relative to the InAs nanowires. No alloy formation is found for samples with faultless oxide layers.
 
Article
A new version of the direct-methods program SnB has been developed. This version incorporates the triplet sieve method for phasing centrosymmetric structures in a way that is transparent to users. The triplet sieve procedure may decrease significantly the time required to achieve a solution for such structures.
 
Article
While channel-cut crystals, in which the diffracting surfaces in an asymmetric cut are kept parallel, can provide beam collimation and spectral beam shaping, they can in addition provide beam compression or expansion if the cut is V-shaped. The compression/expansion ratio depends in this case on the total asymmetry factor. If the Ge(220) diffraction planes and a total asymmetry factor in excess of 10 are used, the rocking curves of two diffractors will have a sufficient overlap only if the second diffractor is tuned slightly with respect to the first one. This study compares and analyses several ways of overcoming this mismatch, which is due to refraction, when the Cu K α 1 beam is compressed 21-fold in a V21 monochromator. A more than sixfold intensity increase was obtained if the matching was improved either by a compositional variation or by a thermal deformation. This provided an intensity gain compared with the use of a simple slit in a symmetrical channel-cut monochromator. The first attempt to overcome the mismatch by introducing different types of X-ray prisms for the required beam deflection is described as well. The performance of the V-shaped monochromators is demonstrated in two applications. A narrow collimated monochromatic beam obtained in the beam compressing mode was used for high-resolution grazing-incidence small-angle X-ray scattering measurements of a silicon sample with corrupted surface. In addition, a two-dimensional Bragg magnifier, based on two crossed V15 channel monochromators in beam expansion mode and tuned by means of unequal asymmetries, was successfully applied to high-resolution imaging of test structures in combination with a Medipix detector.
 
Article
The structures of micelles of the surfactant polysorbate 80 (Tween 80) in 0–50% aqueous dimethyl sulfoxide (DMSO) solutions (pH 7.2, ionic strength 2.44 m M ) were investigated by means of small-angle X-ray scattering. At DMSO concentrations of 0–20%, core–shell cylinder micelles formed, and at 30–50% DMSO, core–shell discus micelles formed, that is, changing the hydrophobicity of the DMSO solvent mixture changed the micelles from core–shell cylinder micelles to core–shell discus micelles.
 
Article
A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The outcome of this type of analysis can also be cast in the form of a new value, along with associated standard uncertainty, that resembles the value of the well known Flack x parameter. The standard uncertainty we obtain is often about half of the standard uncertainty in the value of the Flack x parameter. The proposed formalism is suited in particular to absolute configuration determination from diffraction data of biologically active (pharmaceutical) compounds where the strongest resonant scattering signal often comes from oxygen. It is shown that a reliable absolute configuration assignment in such cases can be made on the basis of Cu Kalpha data, and in some cases even with carefully measured Mo Kalpha data.
 
Measured loading times [s] versus number of atoms ['n'] for a random set of 2,866 structures, ranging from 10,000 → 100,000 atoms.  
Contact calculation times [s] versus number of atoms ['n'] for a random set of 2,866 structures, ranging from 10,000 → 100,000 atoms.  
Article
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent - a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which provide object-oriented abstractions (based on a hierarchical representation of macromolecules), efficient data structures (e.g.kD-trees), fast implementations of common algorithms (e.g. surface-area calculations), read/write support for Protein Data Bank-related file formats and wrappers for external command-line applications (e.g. Stride). Integration of this code into PyCogent is symbiotic, allowing sequence-based work to benefit from structure-derived data and, reciprocally, enabling structural studies to leverage PyCogent's versatile tools for phylogenetic and evolutionary analyses.
 
Article
For the past five years, the Structural Molecular Biology group at the Stanford Synchrotron Radiation Lightsource (SSRL) has provided general users of the facility with fully remote access to the macromolecular crystallography beamlines. This was made possible by implementing fully automated beamlines with a flexible control system and an intuitive user interface, and by the development of the robust and efficient Stanford automated mounting robotic sample-changing system. The ability to control a synchrotron beamline remotely from the comfort of the home laboratory has set a new paradigm for the collection of high-quality X-ray diffraction data and has fostered new collaborative research, whereby a number of remote users from different institutions can be connected at the same time to the SSRL beamlines. The use of remote access has revolutionized the way in which scientists interact with synchrotron beamlines and collect diffraction data, and has also triggered a shift in the way crystallography students are introduced to synchrotron data collection and trained in the best methods for collecting high-quality data. SSRL provides expert crystallographic and engineering staff, state-of-the-art crystallography beamlines, and a number of accessible tools to facilitate data collection and in-house remote training, and encourages the use of these facilities for education, training, outreach and collaborative research.
 
Article
The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal-organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.
 
Article
Ever since its formulation, the Scherrer formula has been the workhorse for quantifying finite size effects in X-ray scattering. Various aspects of Scherrer-type grain-size analysis are discussed with regard to the characterization of thin films with grazing-incidence scattering methods utilizing area detectors. After a brief review of the basic features of Scherrer analysis, a description of resolution-limiting factors in grazing-incidence scattering geometry is provided. As an application, the CHESS D1 beamline is characterized for typical scattering modes covering length scales from the molecular scale to the nanoscale.
 
Article
Small-angle neutron scattering (SANS) and neutron powder diffraction (ND) techniques were used to study quantitatively the effect of nano-sized precipitates and boron addition on the mechanical properties of low-carbon steels. SANS was used to evaluate nano-sized precipitates, smaller than about 600 Å in diameter, and ND was used to determine the weight fraction of the cementite precipitates. Fine core–shell structured spherical precipitates with an average radius of ~50 Å, such as MnS and/or CuS, surrounded by BN layers were observed in the boron-added (BA) low-carbon steels; fine spherical precipitates with an average radius of ~48 Å were mainly observed in the boron-free (BF) low-carbon steels. In the BA steels, the number of boron precipitates, such as BN, Fe 3 (C,B) and MnS, surrounded by BN layers increased drastically at higher hot-rolling temperatures. The volume fraction of the fine precipitates of the BA steels was higher than that of the BF steels; this difference is related to the rapid growth of the BN layers on the MnS and CuS precipitates. Boron addition to low-carbon steels resulted in a reduction in strength and an improvement in elongation; this behaviour is related to the reduction of the solute carbon and the nitrogen contents in the ferrite matrix caused by the precipitation of BN, as well by the increase in the volume fraction of the cementites.
 
Article
The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B 4 C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.
 
BN-PAGE analysis of membrane proteins with known crystal structures. (a) BN-PAGE and tricine-SDS-PAGE of the 11-subunit bovine heart mitochondrial cytochrome bc 1 complex. Two PAGE gels are shown; the left two lanes are results from a BN-PAGE run and are as labeled; the right lane shows the result from tricine-SDS-PAGE (Schagger, 2006) of the same sample, which gives rise to at least ten bands for the intact bovine bc 1 complex. Purified bovine bc 1 in a buffer (50 mM Tris-HCl pH 8.0 supplemented with 0.66 M sucrose) was diluted to a final concentration of 1 mg ml À1 using the same buffer before a BN-PAGE run. There was no need for additional detergents in the dilution because the purified bovine bc 1 contained a sufficient amount of potassium deoxycholate. The arrow indicates the position of the bovine bc 1 complex in BN-PAGE. (b) BN-PAGE and tricine-SDS-PAGE of the four-subunit bacterial cytochrome bc 1 complex from R. sphaeroides. The Rsbc 1 sample in a buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 200 mM histidine, 0.5% -OG) at a concentration of 1 mg ml À1 was used for BN-PAGE. Two bands were shown by the BN-PAGE as indicated by arrows; the top arrow indicates the position of the three-subunit Rsbc 1 complex dimer and the lower arrow indicates the position of the dissociated subunit 4. Four subunits are shown for the same sample by the tricine-SDS-PAGE as indicated.
BN-PAGE analysis of soluble protein complexes. Three AAA+ proteins were analyzed by BN-PAGE. The E. coli ClpA runs at 146 kDa as a monomer, human fulllength p97 runs at 660 kDa, forming a hexamer, and the p97 N-D1 fragment runs at 440 kDa, also a hexamer.
Expression, purification and characterization of the full-length AfCopB and its N-terminal fragment AfCopB-N. (a) SDS-PAGE gel following the purification procedure of the full-length AfCopB. Protein samples were run on a 4-12% bis-tris gel in a 3-(N-morpholino)propanesulfonic acid (MOPS) buffer. The lane labeled with WC is for the whole cell lysate, M is the crude membrane, Ni is the eluent from the Ni-NTA column and SEC is the purified AfCopB after size exclusion chromatography. The two major bands after Ni-NTA chromatography are the full-length AfCopB and a co-purified N-terminal fragment of AfCopB named AfCopB-N. (b) Elution profile of a full-length AfCopB sample eluted from SEC. The blue line represents the profile for the protein sample from a Superdex 200 column, showing two peaks. The first one is from the full-length AfCopB and the second from the copurified AfCopB-N fragment. The pink line is from commercial molecular weight standards. (c) SDS-PAGE gel following the purification of AfCopB-N. Protein sample was run on a 12% bis-tris gel in MOPS buffer. The lane labeled with WC is for the whole cell lysate, M is crude membrane, Ni is eluent from the Ni-NTA column and SEC is the purified AfCopB302 after SEC. (d ) The SEC profile of AfCopB-N after a Superdex 200 column.
Article
Crystallization has long been one of the bottlenecks in obtaining structural information at atomic resolution for membrane proteins. This is largely due to difficulties in obtaining high-quality protein samples. One frequently used indicator of protein quality for successful crystallization is the monodispersity of proteins in solution, which is conventionally obtained by size exclusion chromatography (SEC) or by dynamic light scattering (DLS). Although useful in evaluating the quality of soluble proteins, these methods are not always applicable to membrane proteins either because of the interference from detergent micelles or because of the requirement for large sample quantities. Here, the use of blue native polyacrylamide gel electrophoresis (BN-PAGE) to assess aggregation states of membrane protein samples is reported. A strong correlation is demonstrated between the monodispersity measured by BN-PAGE and the propensity for crystallization of a number of soluble and membrane protein complexes. Moreover, it is shown that there is a direct correspondence between the oligomeric states of proteins as measured by BN-PAGE and those obtained from their crystalline forms. When applied to a membrane protein with unknown structure, BN-PAGE was found to be useful and efficient for selecting well behaved proteins from various constructs and in screening detergents. Comparisons of BN-PAGE with DLS and SEC are provided.
 
Molecular model for cholanic acid. Bond angles ( n ) are shown. Torsion angles (# n ) are listed in Table S2. 
Molecular model for c[-Pro-Thr-Aib-(S) 3-hPHe-Abu]. Bond angles ( n ) are shown. Torsion angles (# n ) are listed in Table S3. 
Article
A new procedure for performing structural analysis of crystalline materials from diffraction data, using internal coordinates, is described. For starting information only unit-cell content, space group, chemical formula, molecular connectivity and a limited amount of diffraction data are required. After first selecting a number of solutions using a Monte Carlo approach with severe filters, which reject the most unrealistic solutions, genetic algorithms (crossover and mutations) are applied. In fact, the initial selection step alone is, frequently, a powerful tool for discovering structures, without recourse to the genetic algorithms. The procedure, while suffering from the limitation that connectivity must be known, is effective in cases where direct methods are not applicable because the diffraction data are scarce, are limited to low diffraction angles or are missing in specific portions of the reciprocal space. The main features of the algorithm are described and examples of validation given. The routines are now available as part of the freely distributed general-purpose program TRY . The program is available on the Web at http://www.theochem.unisa.it/try.html.
 
Programs designed to perform effective searches in a unit-cell database.
Article
A database of lattices using the G 6 representation of the Niggli-reduced cell as the search key provides a more robust and complete search than older techniques. Searching is implemented by finding the distance from the probe cell to other cells using a topological embedding of the Niggli reduction in G 6 , so that all cells representing similar lattices will be found. The embedding provides the first fully linear measure of distances between unit cells. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach.
 
Article
A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the ( Q , ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available.
 
Article
A basic prerequisite for in vivo X-ray imaging of the lung is the exact determination of radiation dose. Achieving resolutions of the order of micrometres may become particularly challenging owing to increased dose, which in the worst case can be lethal for the imaged animal model. A framework for linking image quality to radiation dose in order to optimize experimental parameters with respect to dose reduction is presented. The approach may find application for current and future in vivo studies to facilitate proper experiment planning and radiation risk assessment on the one hand and exploit imaging capabilities on the other.
 
Article
Spherical analyzers are well known instruments for inelastic X-ray scattering (IXS) experiments. High-resolution IXS experiments almost always use Si single crystals as monochromators and spherical analyzers. At higher energies (>20 keV) Si shows a high energy resolution (<10 meV), at an exact symmetric back-diffraction condition, since the energy resolution is given by the real part of the susceptibility or polarizability. However, at low energies (<10 keV), high energy resolution is difficult to achieve with Si. α-SiO2 (quartz) can be an option, since it offers high energy resolution at low energies. In this work, the characterization of high-quality α-SiO2 is presented. Such characterization is made by high-resolution rocking curve, topography and lattice parameter mapping in different samples from a single block. X-ray optics with α-SiO2 for IXS at lower energies (from 2.5 to 12.6 keV) with medium to high energy resolution (from 90 to 11 meV) are proposed and theoretically exploited.
 
Article
Monte-Carlo (MC) methods, based on random updates and the trial-and-error principle, are well suited to retrieve particle size distributions from small-angle scattering patterns of dilute solutions of scatterers. The size sensitivity of size determination methods in relation to the range of scattering vectors covered by the data is discussed. Improvements are presented to existing MC methods in which the particle shape is assumed to be known. A discussion of the problems with the ambiguous convergence criteria of the MC methods are given and a convergence criterion is proposed, which also allows the determination of uncertainties on the determined size distributions.
 
Article
With the rise in popularity of biological small-angle X-ray scattering (BioSAXS) measurements, synchrotron beamlines are confronted with an ever-increasing number of samples from a wide range of solution conditions. To meet these demands, an increasing number of beamlines worldwide have begun to provide automated liquid-handling systems for sample loading. This article presents an automated sample-loading system for BioSAXS beamlines, which combines single-channel disposable-tip pipetting with a vacuum-enclosed temperature-controlled capillary flow cell. The design incorporates an easily changeable capillary to reduce the incidence of X-ray window fouling and cross contamination. Both the robot-control and the data-processing systems are written in Python. The data-processing code, RAW , has been enhanced with several new features to form a user-friendly BioSAXS pipeline for the robot. The flow cell also supports efficient manual loading and sample recovery. An effective rinse protocol for the sample cell is developed and tested. Fluid dynamics within the sample capillary reveals a vortex ring pattern of circulation that redistributes radiation-damaged material. Radiation damage is most severe in the boundary layer near the capillary surface. At typical flow speeds, capillaries below 2 mm in diameter are beginning to enter the Stokes (creeping flow) regime in which mixing due to oscillation is limited. Analysis within this regime shows that single-pass exposure and multiple-pass exposure of a sample plug are functionally the same with regard to exposed volume when plug motion reversal is slow. The robot was tested on three different beamlines at the Cornell High-Energy Synchrotron Source, with a variety of detectors and beam characteristics, and it has been used successfully in several published studies as well as in two introductory short courses on basic BioSAXS methods.
 
Article
Small-angle X-ray scattering (SAXS) was performed on single-crystal chemical vapor deposition (CVD) diamonds with low nitrogen concentrations, which were fabricated by microwave plasma-assisted chemical vapor deposition at high growth rates. High optical quality undoped 500 µm-thick single-crystal CVD diamonds grown without intentional nitrogen addition proved to be excellent as windows on SAXS cells, yielding parasitic scattering no more intense than a 7.5 µm-thick Kapton film. A single-crystal CVD diamond window was successfully used in a high-pressure SAXS cell.
 
Article
Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the program GASBOR at 5 A resolution (q(max) = 1.25 A(-1)) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8 A resolution from the correctly positioned envelope; four distinct peaks at the 3.2sigma level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (q(max) = 0.25 A(-1)). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination of FSEARCH and WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement.
 
Article
The highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid.
 
Article
The need for fast approximate algorithms for Debye summation arises in computations performed in crystallography, small/wide-angle X-ray scattering and small-angle neutron scattering. When integrated into structure refinement protocols these algorithms can provide significant speed up over direct all-atom-to-all-atom computation. However, these protocols often employ an iterative gradient-based optimization procedure, which then requires derivatives of the profile with respect to atomic coordinates. This article presents an accurate, O ( N ) cost algorithm for the computation of scattering profile derivatives. The results reported here show orders of magnitude improvement in computational efficiency, while maintaining the prescribed accuracy. This opens the possibility to efficiently integrate small-angle scattering data into the structure determination and refinement of macromolecular systems.
 
Article
Modern computing power has made it possible to reconstruct low-resolution, three-dimensional shapes from solution small-angle X-ray scattering (SAXS) data on biomolecules without a priori knowledge of the structure. In conjunction with rapid mixing techniques, SAXS has been applied to time resolve conformational changes accompanying important biological processes, such as biomolecular folding. In response to the widespread interest in SAXS reconstructions, their value in conjunction with such time-resolved data has been examined. The group I intron from Tetrahymena thermophila and its P4-P6 subdomain are ideal model systems for investigation owing to extensive previous studies, including crystal structures. The goal of this paper is to assay the quality of reconstructions from time-resolved data given the sacrifice in signal-to-noise required to obtain sharp time resolution.
 
Article
This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.
 
Article
Errors in the paper by Kanaki, Jackson, Hall-Wilton, Piscitelli, Kirstein & Andersen [ J. Appl. Cryst. (2013), 46 , 1031–1037] are corrected.
 
Article
A general theoretical approach to the description of epitaxial layers with essentially different cell parameters and in-plane relaxation anisotropy has been developed. A covariant description of relaxation in such structures has been introduced. An iteration method for evaluation of these parameters on the basis of the diffraction data set has been worked out together with error analysis and reliability checking. The validity of the presented theoretical approaches has been proved with a-ZnO on r-sapphire samples grown in the temperature range from 573 K up to 1073 K. A covariant description of relaxation anisotropy for these samples has been estimated with data measured for different directions of the diffraction plane relative to the sample surface.
 
Article
The new program ANODE estimates anomalous or heavy-atom density by reversing the usual procedure for experimental phase determination by methods such as single- and multiple-wavelength anomalous diffraction and single isomorphous replacement anomalous scattering. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase. The required native phase is calculated from the information in a Protein Data Bank file of the structure. The resulting density enables even very weak anomalous scatterers such as sulfur to be located. Potential applications include the identification of unknown atoms and the validation of molecular replacement solutions.
 
Article
The PGALRS (pseudo-Gaussian approximation to Lee-Richards surfaces) algorithm is discussed. By modeling electron density with unphysical pseudo-Gaussian atoms, the Lee-Richards surface can be approximated by a contour level of that density in time approximately linear in the number of atoms. Having that contour level, the atoms and residues closest to that surface can be identified in average time O[n(2/3)log(n)] using a NearTree-based nearest neighbor search. If a high-quality Lee-Richards surface is required, then, as a final stage, one of the standard Lee-Richards algorithms can be used but considering only the previously identified surface residues; the typical cost is thereby reduced to O[n(2/3)log(n)], making the overall average time for all the steps O(n). For very large macromolecules, such a reduction in computational burden may be essential to being able to render a meaningful molecular surface. This approach extends the feasible range of application for existing molecular surface software, such as MSMS, to larger macromolecules, especially to macromolecules with more than 50 000 atoms, and can be used as a starting point for surface-based (as opposed to backbone-based) motif identification, e.g. using ProMol.
 
Article
The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL . A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.
 
Article
A computer program called ARPGE written in Python uses the theoretical results generated by the computer program GenOVa to automatically reconstruct the parent grains from electron backscatter diffraction data obtained on phase transition materials with or without residual parent phase. The misorientations between daughter grains are identified with operators, the daughter grains are identified with indexed variants, the orientations of the parent grains are determined, and some statistics on the variants and operators are established. Some examples with martensitic transformations in iron and titanium alloys were treated. Variant selection phenomena were revealed.
 
Article
High-throughput crystallography has reached a level of automation where complete computer-assisted robotic crystallization pipelines are capable of cocktail preparation, crystallization plate setup, and inspection and interpretation of results. While mounting of crystal pins, data collection and structure solution are highly automated, crystal harvesting and cryocooling remain formidable challenges towards full automation. To address the final frontier in achieving fully automated high-throughput crystallography, the prototype of an anthropomorphic six-axis universal micromanipulation robot (UMR) has been designed and tested; this UMR is capable of operator-assisted harvesting and cryoquenching of protein crystals as small as 10 microm from a variety of 96-well plates. The UMR is equipped with a versatile tool exchanger providing full operational flexibility. Trypsin crystals harvested and cryoquenched using the UMR have yielded a 1.5 A structure demonstrating the feasibility of robotic protein crystal harvesting.
 
Article
A new easy-to-use device has been designed and implemented for electric field-induced protein crystallization in a vapor-diffusion configuration. The device not only controls crystal nucleation by means of the electrical current, but also favors crystal growth owing to its vapor-diffusion setup. Crystallization was conducted in the presence of an internal electric field and direct current. The proteins investigated were lysozyme, as model protein, and 2TEL-lysozyme (a synthetic protein consisting of two tandem alpha helix motifs connected to a lysozyme moiety). Lysozyme crystals that grew attached to the cathode were larger than those grown attached to the anode or in the absence of an electric current. On the other hand, crystals of 2TEL-lysozyme qualitatively showed a better X-ray diffraction pattern when grown in the presence of an electric current.
 
Article
The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren-Averbach method.
 
Article
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.
 
Article
Constructing a model lattice to fit the observed Bragg diffraction pattern is straightforward for perfect samples, but indexing can be challenging when artifacts are present, such as poorly shaped spots, split crystals giving multiple closely aligned lattices and outright superposition of patterns from aggregated microcrystals. To optimize the lattice model against marginal data, refinement can be performed using a subset of the observations from which the poorly fitting spots have been discarded. Outliers are identified by assuming a Gaussian error distribution for the best-fitting spots and points diverging from this distribution are culled. The set of remaining observations produces a superior lattice model, while the rejected observations can be used to identify a second crystal lattice, if one is present. The prevalence of outliers provides a potentially useful measure of sample quality. The described procedures are implemented for macromolecular crystallography within the autoindexing program labelit.index (http://cci.lbl.gov/labelit).
 
Article
Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05-0.20°) are combined with goniometer tilts at a coarse step (2.0-3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.
 
Article
The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g. cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known as FibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features of FibreFix are outlined and some of its applications are illustrated.
 
Article
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
 
Article
The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.
 
Article
Improved methods for indexing diffraction patterns from macromolecular crystals are presented. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the process. Rapid indexing, without the need for visual inspection, will play an important role as beamlines at synchrotron sources prepare for high-throughput automation.
 
Article
Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.
 
A screenshot showing part of the 'HR chemical space' display. Here the commercial screens used in the 1536 cocktails are arranged in a pre-defined grid according to the most appropriate chemical space. 
Article
A program, AutoSherlock , has been developed to present crystallization screening results in terms of chemical space. This facilitates identification of lead conditions, rational interpretation of results and directions for the optimization of crystallization conditions.
 
Article
Microstructure reconstructions resulting from diffraction contrast tomography data of polycrystalline bulk strontium titanate were reinvestigated by means of electron backscatter diffraction (EBSD) characterization. Corresponding two-dimensional grain maps from the two characterization methods were aligned and compared, focusing on the spatial resolution at the internal interfaces. The compared grain boundary networks show a remarkably good agreement both morphologically and in crystallographic orientation. Deviations are critically assessed and discussed in the context of diffraction data reconstruction and EBSD data collection techniques.
 
Article
The interatomic distance distribution, P(r), is a valuable tool for evaluating the structure of a molecule in solution and represents the maximum structural information that can be derived from solution scattering data without further assumptions. Most current instrumentation for scattering experiments (typically CCD detectors) generates a finely pixelated two-dimensional image. In contin-uation of the standard practice with earlier one-dimensional detectors, these images are typically reduced to a one-dimensional profile of scattering inten-sities, I(q), by circular averaging of the two-dimensional image. Indirect Fourier transformation methods are then used to reconstruct P(r) from I(q). Substantial advantages in data analysis, however, could be achieved by directly estimating the P(r) curve from the two-dimensional images. This article describes a Bayesian framework, using a Markov chain Monte Carlo method, for estimating the parameters of the indirect transform, and thus P(r), directly from the two-dimensional images. Using simulated detector images, it is demonstrated that this method yields P(r) curves nearly identical to the reference P(r). Furthermore, an approach for evaluating spatially correlated errors (such as those that arise from a detector point spread function) is evaluated. Accounting for these errors further improves the precision of the P(r) estimation. Experimental scattering data, where no ground truth reference P(r) is available, are used to demonstrate that this method yields a scattering and detector model that more closely reflects the two-dimensional data, as judged by smaller residuals in cross-validation, than P(r) obtained by indirect transformation of a one-dimensional profile. Finally, the method allows concurrent estimation of the beam center and D max, the longest interatomic distance in P(r), as part of the Bayesian Markov chain Monte Carlo method, reducing experimental effort and providing a well defined protocol for these parameters while also allowing estimation of the covariance among all parameters. This method provides parameter estimates of greater precision from the experimental data. The observed improvement in precision for the traditionally problematic D max is particularly noticeable.
 
Article
Confocal microscopy, a technique that has been extensively applied in cellular biological studies, may also be applied to the visualization and three-dimensional imaging of protein crystals at high resolution on synchrotron beamlines. Protein crystal samples are examined using a commercially available confocal microscope adapted for cryogenic use. A preliminary test using a custom confocal design adapted for beamline use is also presented. The confocal optics configuration is compatible with nonlinear imaging techniques such as two-photon excited fluorescence imaging and second harmonic generation. The possibilities of this method are explored using two modes: fluorescence and reflection confocal. In fluorescence mode, small amounts of dye are introduced into the crystal through soaking or growth conditions. Under such conditions, protein crystals are easily resolved from salts and amorphous precipitates, which do not generally take up dye. Reflection mode, which does not require dye, still exhibits greater resolution and sensitivity to surface detail than conventional wide-field microscopy as a result of the confocal optics configuration. The inherent three-dimensional nature of the method means that on-axis sample views (along the direction of the X-ray beam) can be reconstructed from an off-axis configuration, simplifying the beamline setup and providing uniquely detailed views of cryogenically cooled crystals.
 
Article
This paper reports on several developments of X-ray fluorescence techniques for macromolecular crystallography recently implemented at the National Institute of General Medical Sciences and National Cancer Institute beamlines at the Advanced Photon Source. These include (i) three-band on-the-fly energy scanning around absorption edges with adaptive positioning of the fine-step band calculated from a coarse pass; (ii) on-the-fly X-ray fluorescence rastering over rectangular domains for locating small and invisible crystals with a shuttle-scanning option for increased speed; (iii) fluorescence rastering over user-specified multi-segmented polygons; and (iv) automatic signal optimization for reduced radiation damage of samples.
 
Article
Grazing-incidence X-ray diffraction measurements on single GaAs nanowires (NWs) grown on a (111)-oriented GaAs substrate by molecular beam epitaxy are reported. The positions of the NWs are intentionally determined by a direct implantation of Au with focused ion beams. This controlled arrangement in combination with a nanofocused X-ray beam allows the in-plane lattice parameter of single NWs to be probed, which is not possible for randomly grown NWs. Reciprocal space maps were collected at different heights along the NW to investigate the crystal structure. Simultaneously, substrate areas with different distances from the Au-implantation spots below the NWs were probed. Around the NWs, the data revealed a 0.4% decrease in the lattice spacing in the substrate compared with the expected unstrained value. This suggests the presence of a compressed region due to Au implantation.
 
Article
Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL, for Bravais lattice determination. Results from BGAOL are compared with results from other metric based Bravais lattice determination algorithms. This embedding depends on understanding the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G 6. This article describes an investigation of the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G 6 by algebraic analysis and organized random probing of regions near one-, two-, three-, four-, five-, six-, seven- and eightfold boundary polytope intersections. The discussion of valid boundary polytopes is limited to those avoiding the mathematically interesting but crystallographically impossible cases of zero-length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to zero or without neighboring probe points are eliminated. In all, 216 boundary polytopes are found. There are 15 five-dimensional boundary polytopes of the full G 6 Niggli cone N .
 
Top-cited authors
Louis Farrugia
  • University of Glasgow
Giovanni Luca Cascarano
  • Italian National Research Council
Angela Altomare
  • Institute of Crystallography
Janet Thornton
  • Ashford University
Roman Aleksander Laskowski
  • European Molecular Biology Laboratory