Abstract: The Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.

Abstract: Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.

Abstract: Since the late 1950's, high-pressure structural studies have become increasingly frequent, following the inception of opposed-anvil cells, development of efficient diffractometric equipment (brighter radiation sources both in laboratories and in synchrotron facilities, highly efficient area detectors) and procedures (for crystal mounting, centring, pressure calibration, collecting and correcting data). Consequently, during the last decades, high-pressure crystallography has evolved into a powerful technique which can be routinely applied in laboratories and dedicated synchrotron and neutron facilities. The variation of pressure adds a new thermodynamic dimension to crystal-structure analyses, and extends the understanding of the solid state and materials in general. New areas of thermodynamic exploration of phase diagrams, polymorphism, transformations between different phases and cohesion forces, structure–property relations, and a deeper understanding of matter at the atomic scale in general are accessible with the high-pressure techniques in hand. A brief history, guidelines and requirements for performing high-pressure structural studies are outlined.

Abstract: An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these `Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.

Abstract: New and concise descriptors of the residual density are presented, namely the gross residual electrons, the net residual electrons and the fractal dimension distribution. These descriptors indicate how much residual density is present and in what way it is distributed, i.e. the extent to which the distribution is featureless. The amount of residual density present accounts for noise in the experimental data as well as for modeling inadequacies. Therefore, the minimization of the gross residual electrons during refinement serves as a quality criterion. In the case where only Gaussian noise is present in the residual density, the fractal distribution is parabolic in shape. Deviations from this shape therefore serve as an indicator for systematic errors. The new measures have been applied to simulated and experimental data in order to study the effects of noise, model inadequacies and truncation in the experimental resolution. These measures, although designed and examined with particular regard to applications of space residual density, are very general and can in principle also be applied to space and momentum residual densities in a one-, two-, three- or higher-dimensional Euclidean space.

Abstract: We report on progress in algorithms for iterative phase retrieval. The theory of convex optimization is used to develop and to gain insight into counterparts for the nonconvex problem of phase retrieval. We propose a relaxation of averaged alternating reflectors and determine the fixed point set of the related operator in the convex case. A numerical study supports our theoretical observations and demonstrates the effectiveness of the algorithm compared to the current state of the art.

Abstract: It is demonstrated that a common-line method can assemble a three-dimensional oversampled diffracted intensity distribution suitable for high-resolution structure solution from a set of measured two-dimensional diffraction patterns, as proposed in experiments with an X-ray free-electron laser (XFEL) [Neutze et al. (2000). Nature (London), 406, 752–757]. Even for a flat Ewald sphere, it is shown how the ambiguities due to Friedel's law may be overcome. The method breaks down for photon counts below about 10 per detector pixel, almost three orders of magnitude higher than expected for scattering by a 500 kDa protein with an XFEL beam focused to a 0.1 µm diameter spot. Even if 103 orientationally similar diffraction patterns could be identified and added to reach the requisite photon count per pixel, the need for about 106 orientational classes for high-resolution structure determination suggests that about 109 diffraction patterns must be recorded. Assuming pulse and readout rates of ∼100 Hz, such measurements would require ∼107 s, i.e. several months of continuous beam time.

Abstract: Anisotropic displacement parameters (ADPs) are compared for H atoms estimated using three recently described procedures, both among themselves and with neutron diffraction results. The results convincingly demonstrate that all methods are capable of giving excellent results for several benchmark systems and identify systematic discrepancies for several atom types. A revised and extended library of internal H-atom mean-square displacements is presented for use with Madsen's SHADE web server [J. Appl. Cryst. (2006), 39, 757–758; http://shade.ki.ku.dk], and the improvement over the original SHADE results is substantial, suggesting that this is now the most readily and widely applicable of the three approximate procedures. Using this new library – SHADE2 – it is shown that, in line with expectations, a segmented rigid-body description of the heavy atoms yields only a small improvement in the agreement with neutron results. The SHADE2 library, now incorporated in the SHADE web server, is recommended as a routine procedure for deriving estimates of H-atom ADPs suitable for use in charge-density studies on molecular crystals, and its widespread use should reveal remaining deficiencies and perhaps overcome the inherent bias in the majority of such studies.

Abstract: Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 A. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3 configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.

Abstract: Several flaviviruses are important human pathogens, including dengue virus, a disease against which neither a vaccine nor specific antiviral therapies currently exist. During infection, the flavivirus RNA genome is translated into a polyprotein, which is cleaved into several components. Nonstructural protein 3 (NS3) carries out enzymatic reactions essential for viral replication, including proteolysis of the polyprotein through its serine protease N-terminal domain, with a segment of 40 residues from the NS2B protein acting as a cofactor. The ATPase/helicase domain is located at the C terminus of NS3. Atomic structures are available for these domains separately, but a molecular view of the full-length flavivirus NS3 polypeptide is still lacking. We report a crystallographic structure of a complete NS3 molecule fused to 18 residues of the NS2B cofactor at a resolution of 3.15 A. The relative orientation between the protease and helicase domains is drastically different than the single-chain NS3-NS4A molecule from hepatitis C virus, which was caught in the act of cis cleavage at the NS3-NS4A junction. Here, the protease domain sits beneath the ATP binding site, giving the molecule an elongated shape. The domain arrangement found in the crystal structure fits nicely into an envelope determined ab initio using small-angle X-ray scattering experiments in solution, suggesting a stable molecular conformation. We propose that a basic patch located at the surface of the protease domain increases the affinity for nucleotides and could also participate in RNA binding, explaining the higher unwinding activity of the full-length enzyme compared to that of the isolated helicase domain.

Abstract: Following the seminal work of Von Dreele, powder X-ray diffraction studies on proteins are being established as a valuable complementary technique to single-crystal measurements. A wide range of small proteins have been found to give synchrotron powder diffraction profiles where the peak widths are essentially limited only by the instrumental resolution. The rich information contained in these profiles, combined with developments in data analysis, has stimulated research and development to apply the powder technique to microcrystalline protein samples. In the present work, progress in using powder diffraction for macromolecular crystallography is reported.

Abstract: Structural studies of materials with nano-sized spaces, called nano-structured materials, have been carried out by high-resolution powder diffraction. Our developed analytical method, which is the combination of the maximum-entropy method (MEM) and Rietveld refinement, the so-called MEM/Rietveld method, has been successfully applied to the analysis of synchrotron-radiation (SR) powder diffraction data measured at SPring-8, a third-generation SR light source. In this article, structural studies of nano-porous coordination polymers and endohedral metallofullerenes are presented with the advanced technique of SR powder experiment. The structure of the adsorbed guest molecule in the coordination polymer and encapsulated atoms in the fullerene cage are clearly revealed by the MEM charge density. The methodology of MEM/Rietveld analysis is also presented.

Abstract: The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

Abstract: Structural conversion of the nucleosome, a minimum unit of chromatin structure made up of histones and DNA, has critical effects on DNA-mediated reactions. The mechanism of nucleosome assembly and disassembly has been elusive but now the crystal structure of a histone chaperone in complex with histones H3 and H4 has been determined. CIA (CCG1-interacting factor A)/ASF1, which is the most conserved histone chaperone among the eukaryotes, was genetically identified as a factor for an anti-silencing function (Asf1)1 by yeast genetic screening. Shortly after that, the CIA–histone-H3–H4 complex was isolated from Drosophila as a histone chaperone CAF-1 stimulator2. Human CIA-I/II (ASF1a/b) was identified as a histone chaperone that interacts with the bromodomain—an acetylated-histone-recognizing domain—of CCG1, in the general transcription initiation factor TFIID3,4,5. Intensive studies have revealed that CIA/ASF1 mediates nucleosome assembly by forming a complex with another histone chaperone in human cells6 and yeast7, and is involved in DNA replication1,2, transcription4,8,9,10, DNA repair1,2,11,12 and silencing/anti-silencing1,2,8,13,14,15 in yeast. CIA/ASF1 was shown as a major storage chaperone for soluble histones in proliferating human cells6,16. Despite all these biochemical and biological functional analyses, the structure–function relationship of the nucleosome assembly/disassembly activity of CIA/ASF1 has remained elusive. Here we report the crystal structure, at 2.7 A resolution, of CIA-I in complex with histones H3 and H4. The structure shows the histone H3–H4 dimer's mutually exclusive interactions with another histone H3–H4 dimer and CIA-I. The carboxy-terminal β-strand of histone H4 changes its partner from the β-strand in histone H2A to that of CIA-I through large conformational change. In vitro functional analysis demonstrated that CIA-I has a histone H3–H4 tetramer-disrupting activity. Mutants with weak histone H3–H4 dimer binding activity showed critical functional effects on cellular processes related to transcription. The histone H3–H4 tetramer-disrupting activity of CIA/ASF1 and the crystal structure of the CIA/ASF1–histone-H3–H4 dimer complex should give insights into mechanisms of both nucleosome assembly/disassembly and nucleosome semi-conservative replication.

Abstract: How antimicrobial peptides form pores in membranes is of interest as a fundamental membrane process. However, the underlying molecular mechanism, which has potential applications in therapeutics, nonviral gene transfer, and drug delivery, has been in dispute. We have resolved this mechanism by observing the time-dependent process of pore formation in individual giant unilamellar vesicles (GUVs) exposed to a melittin solution. An individual GUV first expanded its surface area at constant volume and then suddenly reversed to expanding its volume at constant area. The area expansion, the volume expansion, and the point of reversal all match the results of equilibrium measurements performed on peptide–lipid mixtures. The mechanism includes a negative feedback that makes peptide-induced pores stable with a well defined size, contrary to the suggestion that peptides disintegrate the membrane in a detergent-like manner.

Abstract: Methods of contrast variation are tools that are essential in macromolecular structure research. Anomalous dispersion of X-ray diffraction is widely used in protein crystallography. Recent attempts to extend this method to native resonant labels like sulfur and phosphorus are promising. Substitution of hydrogen isotopes is central to biological applications of neutron scattering. Proton spin polarization considerably enhances an existing contrast prepared by isotopic substitution. Concepts and methods of nuclear magnetic resonance (NMR) become an important ingredient in neutron scattering from dynamically polarized targets.

Abstract: Perdeuteration of proteins is becoming more commonplace and the assumption is in general that deuteration does not affect protein structure. In this work, the effect of deuteration on structure is examined by data mining, largely of the Cambridge Structural Database but also of the Inorganic Crystal Structure Database, for deuterated and hydrogenated pairs of small-molecule structures analysed by neutron and X-ray crystallography. Differences between these small-molecule structures have been calculated and the results thus far follow the initial assumption. However, functional changes are known, e.g. D2O is toxic to living systems but H2O is not, kinetics change, small pH to pD changes occur, proteins stiffen in D2O and ferroelectrics alter their properties.

Abstract: The regulation of calcite mineralization by chiral biological molecules is one of the fundamental unresolved issues at the interface between biological, geological, and physical sciences. Here we address the role of chirality of l-aspartic acid (l-Asp), a model additive, in the regulation of the growth of calcite crystals. We apply phase-shift interferometry to nonintrusively monitor in-situ the morphology of the surface and quantify the velocity of propagation of the edges of the unfinished crystal layers, the steps, during crystallization. We show that l-Asp leads to several-fold increase in the step velocity, in all directions, at low supersaturations, and several-fold decrease in the step velocity at high supersaturations. l-Asp also introduces asymmetry in the velocity of steps related by mirror symmetry, however, of ≤10%. To explain the complex effects of l-Asp and, likely, of other biological regulators of calcite crystallization, we show that prior to incorporation into steps, calcium and carbonat...

Abstract: Aizu's characterization of the 773 species of phase transitions by magnetization, polarization and strain is extended to include characterization by the recently observed toroidal moment. The resulting distinction quadruplet characterization is then used to classify the species into sub-ensembles, extending Schmid's concept of ensembles of species to include classification by toroidal moments. Tables are given of the distinction quadruplet characterization of each species and the species in each ensemble and sub-ensemble. The form of primary and secondary ferroic property tensors invariant under the 122 magnetic point groups have also been tabulated for use in determining the characterization of species and possible domain switching. In both cases, physical property tensors related to the toroidal moment are included.

Abstract: 4 as problem to be solved. We determined a crystal structure of a complex of ArgRS from Pyrococcus horikoshii, tRNACCU and ATP analog with Rfactor = 0.215 (Rfree = 0.259) at 2.0 Å resolution and could give one solution for this problem using newly obtained structural information about position of ATP. The experimental results show that the ArgRS protein lacking the additional N-terminal domain characteristic for ArgRS possesses sufficient catalytic activity in the aminoacylation reaction for tRNA. Modeling of relative positions of amino acid, Ade76 of tRNA and ATP on ArgRS was made to find the suitable position to tRNA-assisted formation mechanism of Arg-AMP. It was found that formation of hydrogen bond between 2’OH of Ade76 of tRNA and O2 of carboxy group -C-O2H=O1 of arginine can be achieved in one conformation by rotation around C α-C of carboxy group. In ATP-PPi exchange reaction at low pH, reversible conversion between C=O1 and C-O1-Pα is controlled by the formation of this hydrogen bond. On the other hand, at pH8.0, experimental results in the deacylation reaction of Arg-tRNA is also understood by mechanism that NH of guanidium group -NH=C(NH2)2 of Arg-tRNA donates a proton to C=O2 of ester bond of ArgtRNA, resulting in carbonium C-O2H. We discuss in detail these mechanisms.

Abstract: An empirical relationship of use in prediction and evaluation is established between the standard uncertainty of the Flack parameter and the Bijvoet intensity ratio. The expected value of this ratio may be calculated from the chemical composition of the compound and the X-ray wavelength. Structure analyses published with intensity data have allowed various properties of the Bijvoet intensity ratio to be studied. It is found that, although the Bijvoet intensity ratio has a strong dependence on sin theta/lambda, extrapolation to sin theta/lambda = 0 of model intensity pairs leads to values satisfactorily close to those expected. Moreover, it is shown that there is no symmetry enhancement for general reflections of the Bijvoet ratio in agreement with theory. The behaviour of some special reflections is examined. Two methods of correcting the observed Bijvoet ratio for systematic and random effects have been tested and found to be unsatisfactory. Evidence is produced to show that standard uncertainties provided with intensities are unrealistic and that measurement protocols need improvement.

Abstract: Electron-density maps are calculated by Fourier syntheses with coefficients based on structure factors. Diffraction experiments provide intensities up to a limited resolution; as a consequence, the Fourier syntheses always show series-termination errors. The worse the resolution, the less accurate is the Fourier representation of the electron density. In general, each atomic peak is shifted from the correct position, shows a deformed (with respect to the true distribution of the electrons in the atomic domain) profile, and is surrounded by a series of negative and positive ripples of gradually decreasing amplitude. An algorithm is described which is able to reduce the resolution bias by relocating the peaks in more correct positions and by modifying the peak profile to better fit the real atomic electron densities. Some experimental tests are performed showing the usefulness of the procedure.