http://journals.iucr.org/s/journalhomepage.html Synchrotron radiation sources and their associated technologies have expanded at an extremely rapid rate during the past 20 years. Through the 1990s, many new synchrotron radiation sources have been constructed and exploited worldwide. The Journal of Synchrotron Radiation aims to provide a focus in this rapidly expanding area. The topics covered by the journal include source technology, instrumentation and techniques over all the spectral ranges relevant to synchrotron radiation research. It thus draws together the full breadth of interests and skills of the synchrotron radiation community. Contributions are invited within the general areas of instrumentation, methods and novel applications. The instrumentation topics include: synchrotron radiation sources and beamlines; optics; detectors; electronics and data acquisition; sample chambers and environment. The methods and applications topics are grouped within the following categories; diffraction; spectroscopy, imaging. en-gb Copyright (c) 2008 International Union of Crystallography International Union of Crystallography International Union of Crystallography http://journals.iucr.org urn:issn:0909-0495 Synchrotron radiation sources and their associated technologies have expanded at an extremely rapid rate during the past 20 years. Through the 1990s, many new synchrotron radiation sources have been constructed and exploited worldwide. The Journal of Synchrotron Radiation aims to provide a focus in this rapidly expanding area. The topics covered by the journal include source technology, instrumentation and techniques over all the spectral ranges relevant to synchrotron radiation research. It thus draws together the full breadth of interests and skills of the synchrotron radiation community. Contributions are invited within the general areas of instrumentation, methods and novel applications. The instrumentation topics include: synchrotron radiation sources and beamlines; optics; detectors; electronics and data acquisition; sample chambers and environment. The methods and applications topics are grouped within the following categories; diffraction; spectroscopy, imaging. text/html Open access article in Journal of Synchrotron Radiation text yearly 6 2002-01-01T00:00+00:00 med@iucr.org Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 http://journals.iucr.org/logos/rss10s.gif http://journals.iucr.org/s/journalhomepage.html Still image http://scripts.iucr.org/cgi-bin/paper?me0369 Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 , 2008-07-01 doi:10.1107/S0909049508017330 International Union of Crystallography en text/html Current events text 4 15 2008-07-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography current events 423 424 http://scripts.iucr.org/cgi-bin/paper?me0368 Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 , 2008-05-01 doi:10.1107/S0909049508009175 International Union of Crystallography en text/html Current events text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography current events 319 321 http://scripts.iucr.org/cgi-bin/paper?ys5026 A new detector system for protein crystallography is now being developed based on an X-ray HARP–FEA (high-gain avalanche rushing amorphous photoconductor–field emitter array), which consists of an amorphous selenium membrane and a matrix field emitter array. The combination of the membrane avalanche effect with a single driven FEA has several advantages over currently available area detectors, including higher sensitivity, higher spatial resolution and a higher frame rate. Preliminary evaluation of the detector has been carried out and its effectiveness has been confirmed. Next, diffraction images were measured with continuous rotation of a protein crystal, and the images were compared with those measured by the existing CCD detector; the system successfully obtained high-spatial-resolution images. Using shutterless measurement, the total measurement time can be reduced significantly, making the method appropriate for high-throughput protein crystallography. The X-ray HARP–FEA detector is an attractive candidate for the next generation of X-ray area detectors. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Miyoshi, T. Igarashi, N. Matsugaki, N. Yamada, Y. Hirano, K. Hyodo, K. Tanioka, K. Egami, N. Namba, M. Kubota, M. Kawai, T. Wakatsuki, S. 2008-05-01 doi:10.1107/S0909049508006584 International Union of Crystallography A new detector system for protein crystallography based on an X-ray HARP–FEA is presented. en HARP; SEMICONDUCTOR; AMORPHOUS SELENIUM; AVALANCHE MULTIPLICATION; IMAGING DEVICE; PROTEIN CRYSTALLOGRAPHY A new detector system for protein crystallography is now being developed based on an X-ray HARP–FEA (high-gain avalanche rushing amorphous photoconductor–field emitter array), which consists of an amorphous selenium membrane and a matrix field emitter array. The combination of the membrane avalanche effect with a single driven FEA has several advantages over currently available area detectors, including higher sensitivity, higher spatial resolution and a higher frame rate. Preliminary evaluation of the detector has been carried out and its effectiveness has been confirmed. Next, diffraction images were measured with continuous rotation of a protein crystal, and the images were compared with those measured by the existing CCD detector; the system successfully obtained high-spatial-resolution images. Using shutterless measurement, the total measurement time can be reduced significantly, making the method appropriate for high-throughput protein crystallography. The X-ray HARP–FEA detector is an attractive candidate for the next generation of X-ray area detectors. text/html Development of an X-ray HARP–FEA detector system for high-throughput protein crystallography text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 281 284 http://scripts.iucr.org/cgi-bin/paper?ys5019 Six-transmembrane (6-TM) cation channels are plasma membrane-integral components of cellular signaling pathways conserved in almost all species, including animals, plants and some kinds of prokaryotes. These channels selectively permeate cations in response to various signals. In excitable and non-excitable mammalian cells, 6-TM cation channels play fundamental roles, including the generation of action potential and its transmission, the regulation of intracellular ion concentrations, and the activation of signaling cascades by humoral or mechanical pathways. Recently, the structures of three different 6-TM-type cation channels have been determined using single-particle analysis from cryo-electron microscopy images: the voltage-sensitive sodium channel, the IP3 receptor and the TRPC3 channel. The basic structure of the molecules is similar: a bell-like shape comprising a relatively small extracellular (or luminal) domain, a protein-dense transmembrane domain and an expanded cytoplasmic domain. However, in detail, the cytoplasmic architectures are different from one another and are diversely evolved to their specific physiological functions. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Mio, K. Ogura, T. Sato, C. 2008-05-01 doi:10.1107/S0909049508004640 International Union of Crystallography Single-particle analysis is a computer-aided method for determining protein structure using projection images obtained by electron microscopy. Recently reconstructed 6-TM-type cation channels demonstrate the structural similarities and divergence of the family. en ELECTRON MICROSCOPY; ION CHANNEL STRUCTURE; SIX-TRANSMEMBRANE; SINGLE PARTICLES Six-transmembrane (6-TM) cation channels are plasma membrane-integral components of cellular signaling pathways conserved in almost all species, including animals, plants and some kinds of prokaryotes. These channels selectively permeate cations in response to various signals. In excitable and non-excitable mammalian cells, 6-TM cation channels play fundamental roles, including the generation of action potential and its transmission, the regulation of intracellular ion concentrations, and the activation of signaling cascades by humoral or mechanical pathways. Recently, the structures of three different 6-TM-type cation channels have been determined using single-particle analysis from cryo-electron microscopy images: the voltage-sensitive sodium channel, the IP3 receptor and the TRPC3 channel. The basic structure of the molecules is similar: a bell-like shape comprising a relatively small extracellular (or luminal) domain, a protein-dense transmembrane domain and an expanded cytoplasmic domain. However, in detail, the cytoplasmic architectures are different from one another and are diversely evolved to their specific physiological functions. text/html Structure of six-transmembrane cation channels revealed by single-particle analysis from electron microscopic images text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 211 214 http://scripts.iucr.org/cgi-bin/paper?ys5027 An attempt has been made to improve a crystal contact of human acidic fibroblast growth factor (haFGF; 140 amino acids) to control the crystal growth, because haFGF crystallizes only as a thin-plate form, yielding crystals suitable for X-ray but not neutron diffraction. X-ray crystal analysis of haFGF showed that the Glu81 side chain, located at a crystal contact between haFGF molecules, is in close proximity with an identical residue related by crystallographic symmetry, suggesting that charge repulsion may disrupt suitable crystal-packing interactions. To investigate whether the Glu residue affects the crystal-packing interactions, haFGF mutants in which Glu81 was replaced by Ala, Val, Leu, Ser and Thr were constructed. Although crystals of the Ala and Leu mutants were grown as a thin-plate form by the same precipitant (formate) as the wild type, crystals of the Ser and Thr mutants were grown with increased thickness, yielding a larger overall crystal volume. X-ray structural analysis of the Ser mutant determined at 1.35 Å resolution revealed that the hydroxy groups of Ser are linked by hydrogen bonds mediated by the formate used as a precipitant. This approach to engineering crystal contacts may contribute to the development of large protein crystals for neutron crystallography. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Honjo, E. Tamada, T. Adachi, M. Kuroki, R. Meher, A. Blaber, M. 2008-05-01 doi:10.1107/S0909049508004470 International Union of Crystallography Several mutations at Glu81 located on the crystal contact of human acidic fibroblast growth factor were studied in an effort to improve crystal growth. Mutation to Ser and Thr resulted in crystallization of a rather bulky form of the wild type, whereas mutation to Val prohibited crystallization. These results suggest that crystal growth may be controlled by designing a new interface by protein engineering. en ACIDIC FIBROBLAST GROWTH FACTOR; CRYSTAL CONTACTS; MUTAGENESIS An attempt has been made to improve a crystal contact of human acidic fibroblast growth factor (haFGF; 140 amino acids) to control the crystal growth, because haFGF crystallizes only as a thin-plate form, yielding crystals suitable for X-ray but not neutron diffraction. X-ray crystal analysis of haFGF showed that the Glu81 side chain, located at a crystal contact between haFGF molecules, is in close proximity with an identical residue related by crystallographic symmetry, suggesting that charge repulsion may disrupt suitable crystal-packing interactions. To investigate whether the Glu residue affects the crystal-packing interactions, haFGF mutants in which Glu81 was replaced by Ala, Val, Leu, Ser and Thr were constructed. Although crystals of the Ala and Leu mutants were grown as a thin-plate form by the same precipitant (formate) as the wild type, crystals of the Ser and Thr mutants were grown with increased thickness, yielding a larger overall crystal volume. X-ray structural analysis of the Ser mutant determined at 1.35 Å resolution revealed that the hydroxy groups of Ser are linked by hydrogen bonds mediated by the formate used as a precipitant. This approach to engineering crystal contacts may contribute to the development of large protein crystals for neutron crystallography. text/html Mutagenesis of the crystal contact of acidic fibroblast growth factor text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 285 287 http://scripts.iucr.org/cgi-bin/paper?me0364 Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 , 2008-03-01 doi:10.1107/S090904950800407X International Union of Crystallography en text/html Current events text 2 15 2008-03-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography current events 195 197 http://scripts.iucr.org/cgi-bin/paper?ys5039 A new type of rotating anticathode X-ray generator has been developed, in which the electron beam irradiates the inner surface of a U-shaped anticathode (Cu). A high-flux electron beam is focused on the inner surface by optimizing the shape of the bending magnet. The power of the electron beam can be increased to the point at which the irradiated part of the inner surface is melted, because a strong centrifugal force fixes the melted part on the inner surface. When the irradiated part is melted, a large amount of energy is stored as the heat of fusion, resulting in emission of X-rays 4.3 times more brilliant than can be attained by a conventional rotating anticathode. Oscillating translation of the irradiated position on the inner surface during use is expected to be very advantageous for extending the target life. A carbon film coating on the inner surface is considered to suppress evaporation of the target metal and will be an important technique in further realization of highly bright X-ray generation. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Sakabe, N. Ohsawa, S. Sugimura, T. Ikeda, M. Tawada, M. Watanabe, N. Sasaki, K. Ohshima, K. Wakatsuki, M. Sakabe, K. 2008-05-01 doi:10.1107/S0909049508003993 International Union of Crystallography A very compact X-ray generator, 4.3 times more brilliant than can be attained by a conventional rotating-anticathode X-ray generator, has been developed using a U-shaped rotating anticathode and a high-flux electron gun with focusing bending magnet. en BRIGHT X-RAY GENERATORS; U-SHAPE ANTICATHODES; HEAT OF FUSION; TARGET LIFE EXTENSION; LOW EMITTANCE; DC/PULSE GUNS; FOCUSING BENDING MAGNETS A new type of rotating anticathode X-ray generator has been developed, in which the electron beam irradiates the inner surface of a U-shaped anticathode (Cu). A high-flux electron beam is focused on the inner surface by optimizing the shape of the bending magnet. The power of the electron beam can be increased to the point at which the irradiated part of the inner surface is melted, because a strong centrifugal force fixes the melted part on the inner surface. When the irradiated part is melted, a large amount of energy is stored as the heat of fusion, resulting in emission of X-rays 4.3 times more brilliant than can be attained by a conventional rotating anticathode. Oscillating translation of the irradiated position on the inner surface during use is expected to be very advantageous for extending the target life. A carbon film coating on the inner surface is considered to suppress evaporation of the target metal and will be an important technique in further realization of highly bright X-ray generation. text/html Highly bright X-ray generator using heat of fusion with a specially designed rotating anticathode text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 231 234 http://scripts.iucr.org/cgi-bin/paper?ys5031 Owing to recent advances in high-throughput technology in macromolecular crystallography beamlines, such as high-brilliant X-ray sources, high-speed readout detectors and robotics, the number of samples that can be examined in a single visit to the beamline has increased dramatically. In order to make these experiments more efficient, two functions, remote monitoring and diffraction image evaluation, have been implemented in the macromolecular crystallography beamlines at the Photon Factory (PF). Remote monitoring allows scientists to participate in the experiment by watching from their laboratories, without having to come to the beamline. Diffraction image evaluation makes experiments easier, especially when using the sample exchange robot. To implement these two functions, two independent clients have been developed that work specifically for remote monitoring and diffraction image evaluation. In the macromolecular crystallography beamlines at PF, beamline control is performed using STARS (simple transmission and retrieval system). The system adopts a client–server style in which client programs communicate with each other through a server process using the STARS protocol. This is an advantage of the extension of the system; implementation of these new functions required few modifications of the existing system. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Yamada, Y. pHonda, N. Matsugaki, N. Igarashi, N. Hiraki, M. Wakatsuki, S. 2008-05-01 doi:10.1107/S0909049508004019 International Union of Crystallography At the Photon Factory macromolecular crystallography beamlines, two new functions, remote monitoring and diffraction image evaluation, have been developed and installed on the beamline controlling system STARS (simple transmission and retrieval system). en MACROMOLECULAR CRYSTALLOGRAPHY; BEAMLINE CONTROL SYSTEM; REMOTE MONITORING; DIFFRACTION IMAGE EVALUATION Owing to recent advances in high-throughput technology in macromolecular crystallography beamlines, such as high-brilliant X-ray sources, high-speed readout detectors and robotics, the number of samples that can be examined in a single visit to the beamline has increased dramatically. In order to make these experiments more efficient, two functions, remote monitoring and diffraction image evaluation, have been implemented in the macromolecular crystallography beamlines at the Photon Factory (PF). Remote monitoring allows scientists to participate in the experiment by watching from their laboratories, without having to come to the beamline. Diffraction image evaluation makes experiments easier, especially when using the sample exchange robot. To implement these two functions, two independent clients have been developed that work specifically for remote monitoring and diffraction image evaluation. In the macromolecular crystallography beamlines at PF, beamline control is performed using STARS (simple transmission and retrieval system). The system adopts a client–server style in which client programs communicate with each other through a server process using the STARS protocol. This is an advantage of the extension of the system; implementation of these new functions required few modifications of the existing system. text/html Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 296 299 http://scripts.iucr.org/cgi-bin/paper?ys5002 The main component of natural teeth was determined many years ago as calcium phosphate, mostly in the form of hydroxyapatite with different crystallites. In the past, the method used in tooth crystal investigation has been mainly powder X-ray diffraction analysis, but this method has its drawbacks, i.e. the destruction of the natural tooth structure and the difficulty in examining the preferred orientation in different layers of the tooth. During the last century, microzone X-ray diffraction on the tooth surface was carried out, but, as the technology was less sophisticated, the results obtained were not very detailed. The newly developed microdiffraction equipment permits analysis of the microzone of teeth in situ. To test this new microdiffraction equipment, microdiffraction analysis of one natural healthy deciduous molar tooth and one carious deciduous molar tooth has been performed, using a Bruker D8 instrument. Phase analysis of the two teeth was performed; the crystal size at six test points in the natural healthy tooth was calculated by reflection (211), and the crystal preferred orientation of reflection (300) and reflection (002) at six test points in the natural healthy tooth were compared. The results showed that the tooth was a kind of biological mixed crystal composed of several crystal phases, the main crystal phase being hydroxyapatite. The crystal size grew larger going from the dentin to the enamel. The crystal preferred orientation mainly existed in the enamel, especially in the reflection (002). From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Xue, J. Zhang, L. Zou, L. Liao, Y. Li, J. Xiao, L. Li, W. 2008-05-01 doi:10.1107/S0909049508003397 International Union of Crystallography In situ microzone X-ray diffraction analysis of natural teeth is presented. From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment. en X-RAY MICRODIFFRACTION; ENAMEL; CARIES; TEXTURE; CRYSTAL The main component of natural teeth was determined many years ago as calcium phosphate, mostly in the form of hydroxyapatite with different crystallites. In the past, the method used in tooth crystal investigation has been mainly powder X-ray diffraction analysis, but this method has its drawbacks, i.e. the destruction of the natural tooth structure and the difficulty in examining the preferred orientation in different layers of the tooth. During the last century, microzone X-ray diffraction on the tooth surface was carried out, but, as the technology was less sophisticated, the results obtained were not very detailed. The newly developed microdiffraction equipment permits analysis of the microzone of teeth in situ. To test this new microdiffraction equipment, microdiffraction analysis of one natural healthy deciduous molar tooth and one carious deciduous molar tooth has been performed, using a Bruker D8 instrument. Phase analysis of the two teeth was performed; the crystal size at six test points in the natural healthy tooth was calculated by reflection (211), and the crystal preferred orientation of reflection (300) and reflection (002) at six test points in the natural healthy tooth were compared. The results showed that the tooth was a kind of biological mixed crystal composed of several crystal phases, the main crystal phase being hydroxyapatite. The crystal size grew larger going from the dentin to the enamel. The crystal preferred orientation mainly existed in the enamel, especially in the reflection (002). From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment. text/html High-resolution X-ray microdiffraction analysis of natural teeth text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 235 238 http://scripts.iucr.org/cgi-bin/paper?ys5034 The crystal structure of a photosystem II (PSII) dimer from Thermosynechococcus vulcanus with its psbTc gene inactivated by insertion mutation of an antibiotic cassette in a site in the C-terminal region was analyzed at 3.8 Å resolution. In the crystal structure of the mutant PSII, the transmembrane helix of PsbTc remains, whereas the C-terminal loop of PsbTc has disappeared. In addition, the PsbM subunit, which seemed to be lost in a PsbTc-deletion mutant PSII of T. elongatus, is still present. The deletion of the C-terminal loop of PsbTc in the mutant PSII was verified by mass spectrometry. Thus, the insertion mutation of psbTc eliminated only the C-terminal loop of this subunit. Nevertheless, some features of the mutant PSII, namely a destabilization of the dimeric form and a slight decrease of the oxygen-evolving activity, were observed in the mutant, indicating that the C-terminal loop of PsbTc functions to maintain the stability of the PSII dimer and the activity of oxygen evolution. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Henmi, T. Iwai, M. Ikeuchi, M. Kawakami, K. Shen, J.-R.. Kamiya, N. 2008-05-01 doi:10.1107/S0909049508002458 International Union of Crystallography The characterization of a PsbTc-truncated mutant photosystem II complex is described. en PHOTOSYSTEM II; PSBTC; OXYGEN EVOLUTION; MUTANT; THERMOSYNECHOCOCCUS VULCANUS The crystal structure of a photosystem II (PSII) dimer from Thermosynechococcus vulcanus with its psbTc gene inactivated by insertion mutation of an antibiotic cassette in a site in the C-terminal region was analyzed at 3.8 Å resolution. In the crystal structure of the mutant PSII, the transmembrane helix of PsbTc remains, whereas the C-terminal loop of PsbTc has disappeared. In addition, the PsbM subunit, which seemed to be lost in a PsbTc-deletion mutant PSII of T. elongatus, is still present. The deletion of the C-terminal loop of PsbTc in the mutant PSII was verified by mass spectrometry. Thus, the insertion mutation of psbTc eliminated only the C-terminal loop of this subunit. Nevertheless, some features of the mutant PSII, namely a destabilization of the dimeric form and a slight decrease of the oxygen-evolving activity, were observed in the mutant, indicating that the C-terminal loop of PsbTc functions to maintain the stability of the PSII dimer and the activity of oxygen evolution. text/html X-ray crystallographic and biochemical characterizations of a mutant photosystem II complex from Thermosynechococcus vulcanus with the psbTc gene inactivated by an insertion mutation text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 304 307 http://scripts.iucr.org/cgi-bin/paper?ys5023 To investigate quantitatively the effects of stirring on protein crystallization, a new stirring system which can agitate a protein solution, ∼100 nl, by providing Hagen–Poiseuille flow has been successfully developed. In addition, this new stirring system provides flow with a well defined pattern and velocity. Using this system, hen egg-white lysozyme was crystallized in 100–200 nl solutions while being stirred. The optimum stirring conditions for lysozyme crystals have been explored by evaluating the Reynolds (Re) number and the crystals obtained. Intermittent flow, as well as a low Re number, was found to contribute significantly to the growth of a smaller number of larger crystals. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Maki, S. Murai, R. Yoshikawa, H.Y. Kitatani, T. Nakata, S. Kawahara, H. Hasenaka, H. Kobayashi, A. Okada, S. Sugiyama, S. Adachi, H. Matsumura, H. Takano, K. Murakami, S. Inoue, T. Sasaki, T. Mori, Y. 2008-05-01 doi:10.1107/S0909049508001842 International Union of Crystallography To investigate quantitatively the effects of stirring on protein crystallization, a new stirring system which can agitate a protein solution, ∼100 nl, by providing Hagen–Poiseuille flow has been successfully developed. en LYSOZYME; LOW-REYNOLDS-NUMBER FLOW; STIRRING METHOD; SYRINGE PUMP; MICROCAPILLARY; THIXOTROPY To investigate quantitatively the effects of stirring on protein crystallization, a new stirring system which can agitate a protein solution, ∼100 nl, by providing Hagen–Poiseuille flow has been successfully developed. In addition, this new stirring system provides flow with a well defined pattern and velocity. Using this system, hen egg-white lysozyme was crystallized in 100–200 nl solutions while being stirred. The optimum stirring conditions for lysozyme crystals have been explored by evaluating the Reynolds (Re) number and the crystals obtained. Intermittent flow, as well as a low Re number, was found to contribute significantly to the growth of a smaller number of larger crystals. text/html Protein crystallization in a 100 nl solution with new stirring equipment text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 269 272 http://scripts.iucr.org/cgi-bin/paper?ys5017 The ATP-dependent protease, FtsH, degrades misassembled membrane proteins for quality control like SecY, subunit a of FoF1-ATPase, and YccA, and digests short-lived soluble proteins in order to control their cellular regulation, including σ32, LpxC and λcII. The FtsH protein has an N-terminal transmembrane segment and a large cytosolic region that consists of two domains, an ATPase and a protease domain. To provide a structural basis for the nucleotide-dependent domain motions and a better understanding of substrate translocation, the crystal structures of the Helicobacter pylori (Hp) FtsH ATPase domain in the nucleotide-free state and complexed with ADP, were determined. Two different structures of HpFtsH ATPase were observed, with the nucleotide-free state in an asymmetric unit, and these structures reveal the new forms and show other conformational differences between the nucleotide-free and ADP-bound state compared with previous structures. In particular, one HpFtsH Apo structure has a considerable rotation difference compared with the HpFtsH ADP complex, and this large conformational change reveals that FtsH may have the mechanical force needed for substrate translocation. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Kim, S.H. Kang, G.B. Song, H.-E. Park, S.J. Bea, M.-H. Eom, S.H. 2008-05-01 doi:10.1107/S090904950706846X International Union of Crystallography The crystal structures of the Helicobacter pylori FtsH ATPase domain in the nucleotide-free state and complexed with ADP have been determined. en ATP-DEPENDENT PROTEASE; FTSH; HELICOBACTER PYLORI The ATP-dependent protease, FtsH, degrades misassembled membrane proteins for quality control like SecY, subunit a of FoF1-ATPase, and YccA, and digests short-lived soluble proteins in order to control their cellular regulation, including σ32, LpxC and λcII. The FtsH protein has an N-terminal transmembrane segment and a large cytosolic region that consists of two domains, an ATPase and a protease domain. To provide a structural basis for the nucleotide-dependent domain motions and a better understanding of substrate translocation, the crystal structures of the Helicobacter pylori (Hp) FtsH ATPase domain in the nucleotide-free state and complexed with ADP, were determined. Two different structures of HpFtsH ATPase were observed, with the nucleotide-free state in an asymmetric unit, and these structures reveal the new forms and show other conformational differences between the nucleotide-free and ADP-bound state compared with previous structures. In particular, one HpFtsH Apo structure has a considerable rotation difference compared with the HpFtsH ADP complex, and this large conformational change reveals that FtsH may have the mechanical force needed for substrate translocation. text/html Structural studies on Helicobacter pylori ATP-dependent protease, FtsH text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 208 210 http://scripts.iucr.org/cgi-bin/paper?ys5020 The Protein Crystallography Station at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. This capability also includes the Macromolecular Neutron Crystallography (MNC) consortium between Los Alamos (LANL) and Lawrence Berkeley National Laboratories for developing computational tools for neutron protein crystallography, a biological deuteration laboratory, the National Stable Isotope Production Facility, and an MNC drug design consortium between LANL and Case Western Reserve University. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Langan, P. Fisher, Z. Kovalevsky, A. Mustyakimov, M. Sutcliffe Valone, A. Unkefer, C. Waltman, M.J. Coates, L. Adams, P.D. Afonine, P.V. Bennett, B. Dealwis, C. Schoenborn, B.P. 2008-05-01 doi:10.1107/S0909049508000824 International Union of Crystallography The capabilities of the Protein Crystallography Station at Los Alamos Neutron Science Center for determining protein structures by spallation neutron crystallography are illustrated, and the methodological and technological advances that are emerging from the Macromolecular Neutron Crystallography consortium are described. en NEUTRONS; PROTEINS; MACROMOLECULAR CRYSTALLOGRAPHY; DEUTERATION; ENZYME MECHANISMS; DRUG BINDING; HYDRATION; JOINT XN STRUCTURE REFINEMENT The Protein Crystallography Station at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. This capability also includes the Macromolecular Neutron Crystallography (MNC) consortium between Los Alamos (LANL) and Lawrence Berkeley National Laboratories for developing computational tools for neutron protein crystallography, a biological deuteration laboratory, the National Stable Isotope Production Facility, and an MNC drug design consortium between LANL and Case Western Reserve University. text/html Protein structures by spallation neutron crystallography text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 215 218 http://scripts.iucr.org/cgi-bin/paper?wl5143 Station 9.8 is one of the most oversubscribed and high-throughput stations at the Synchrotron Radiation Source, Daresbury, whereby awarded experimental time is limited, data collections last normally no longer than an hour, user changeover is normally every 24 h, and familiarity with the station systems can be low. Therefore time lost owing to technical failures on the station has a dramatic impact on productivity. To provide 24 h support, the application of a turnkey communication system has been implemented, and is described along with additional applications including its use for inter-continental classroom instruction, user training and remote participation. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Warren, J.E. Diakun, G. Bushnell-Wye, G. Fisher, S. Thalal, A. Helliwell, M. Helliwell, J.R. 2008-03-01 doi:10.1107/S0909049508000587 International Union of Crystallography The application of a turnkey communication system for telepresence at station 9.8 of the Synchrotron Radiation Source, Daresbury, is described and demonstrated, including its use for inter-continental classroom instruction and user training. en TELEPRESENCE; REMOTE TECHNICAL SUPPORT; WIDENING PARTICIPATION; GICSI INITIATIVE; USER TRAINING; STUDENT TEACHING; REMOTE USER PARTICIPATION Station 9.8 is one of the most oversubscribed and high-throughput stations at the Synchrotron Radiation Source, Daresbury, whereby awarded experimental time is limited, data collections last normally no longer than an hour, user changeover is normally every 24 h, and familiarity with the station systems can be low. Therefore time lost owing to technical failures on the station has a dramatic impact on productivity. To provide 24 h support, the application of a turnkey communication system has been implemented, and is described along with additional applications including its use for inter-continental classroom instruction, user training and remote participation. text/html Science experiments via telepresence at a synchrotron radiation source facility text 2 15 2008-03-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 191 194 http://scripts.iucr.org/cgi-bin/paper?ys5006 With an increasing number of biological macromolecular crystal structures measured at ultrahigh resolution (1 Å or better), it is necessary to extend to large systems the experimental valence electron density modelling that is applied to small molecules. A database of average multipole populations has been built, describing the electron density of chemical groups in all 20 amino acids found in proteins. It allows calculation of atomic aspherical scattering factors, which are the starting point for refinement of the protein electron density, using the MoPro software. It is shown that the use of non-spherical scattering factors has a major impact on crystallographic statistics and results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. It is also possible to obtain a realistic valence electron density model, which is used in the calculation of the electrostatic potential and energetic properties of proteins. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Lecomte, C. Jelsch, C. Guillot, B. Fournier, B. Lagoutte, A. 2008-05-01 doi:10.1107/S0909049508000447 International Union of Crystallography Ultrahigh-resolution protein diffraction data allow valence electron density modelling and calculations of experimental electrostatic properties. Protein–ligand interaction energy may therefore be estimated. en ELECTRON DENSITY; PROTEIN REFINEMENT; HIGH-RESOLUTION CRYSTALLOGRAPHY With an increasing number of biological macromolecular crystal structures measured at ultrahigh resolution (1 Å or better), it is necessary to extend to large systems the experimental valence electron density modelling that is applied to small molecules. A database of average multipole populations has been built, describing the electron density of chemical groups in all 20 amino acids found in proteins. It allows calculation of atomic aspherical scattering factors, which are the starting point for refinement of the protein electron density, using the MoPro software. It is shown that the use of non-spherical scattering factors has a major impact on crystallographic statistics and results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. It is also possible to obtain a realistic valence electron density model, which is used in the calculation of the electrostatic potential and energetic properties of proteins. text/html Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 202 203 http://scripts.iucr.org/cgi-bin/paper?ys5003 For the three complex crystal structures of HIV-1 aspartic protease (an enzyme of AIDS) with its inhibitor in the Protein Data Bank, molecular dynamics of the generalized Born surface area and the ab initio fragment molecular orbital of an ABINIT-MP calculation was performed to obtain the binding free energy, the molecular orbital energy, the interaction energy of residues with an inhibitor and the charge transfer at the active site. The inhibitors are five symmetric cyclic ureas, of which three were modelled, and an asymmetric dipeptide. The interaction energy of the inhibitor at the active sites of aspartic acid is as great as 50 kcal mol−1, coinciding with a tetrahedral transition state. For the inhibitor with a higher affinity, charge was transferred to the inhibitor from the active site. The difference in symmetry of the inhibitor was not evident. Binding free energy corresponds to the experimental value of the binding constant, while molecular orbital energy does not always, which is considered to be an entropy effect. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Koyano, K. Nakano, T. 2008-05-01 doi:10.1107/S0909049507068586 International Union of Crystallography Molecular dynamics and the ab initio fragment molecular orbital method were applied to investigate the interaction of HIV-1 aspartic protease with its inhibitor. The interaction energy of the inhibitor at the active sites of aspartic acid obtained by the ab initio fragment molecular orbital method was as great as 50 kcal mol−1, coinciding with a tetrahedral transition state. en AIDS; ASPARTIC PROTEASE INHIBITOR; MOLECULAR DYNAMICS MM_GBSA; FRAGMENT MOLECULAR ORBITAL ABINIT-MP; TETRAHEDRAL TRANSITION STATES; ACTIVE SITES; INTERACTION ENERGY; CHARGE TRANSFER For the three complex crystal structures of HIV-1 aspartic protease (an enzyme of AIDS) with its inhibitor in the Protein Data Bank, molecular dynamics of the generalized Born surface area and the ab initio fragment molecular orbital of an ABINIT-MP calculation was performed to obtain the binding free energy, the molecular orbital energy, the interaction energy of residues with an inhibitor and the charge transfer at the active site. The inhibitors are five symmetric cyclic ureas, of which three were modelled, and an asymmetric dipeptide. The interaction energy of the inhibitor at the active sites of aspartic acid is as great as 50 kcal mol−1, coinciding with a tetrahedral transition state. For the inhibitor with a higher affinity, charge was transferred to the inhibitor from the active site. The difference in symmetry of the inhibitor was not evident. Binding free energy corresponds to the experimental value of the binding constant, while molecular orbital energy does not always, which is considered to be an entropy effect. text/html Interaction of HIV-1 aspartic protease with its inhibitor, by molecular dynamics and ab initio fragment molecular orbital method text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 239 242 http://scripts.iucr.org/cgi-bin/paper?ys5038 Determination of the appropriate conditions for protein crystallization remains a highly empirical process. Preventing protein aggregation is necessary for the formation of single crystals under aggregation-prone solution conditions. Because many amino acids and amino acid derivatives offer a unique combination of solubility and stabilizing properties, they open new avenues into the field of protein aggregation research. The use of amino acids and amino acid derivatives can potentially influence processes such as heat treatment and refolding reactions. The effect of the addition of several amino acids, such as lysine, and several amino acid derivatives, such as glycine ethyl ester and glycine amide, on the crystallization of equine hemoglobin and bovine pancreatic ribonuclease A has been examined. The addition of these amino acids and amino acid derivatives expanded the range of precipitant concentration in which crystals formed without aggregation. The addition of such additives appears to promote the crystallization of proteins. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Ito, L. Kobayashi, T. Shiraki, K. Yamaguchi, H. 2008-05-01 doi:10.1107/S0909049507068598 International Union of Crystallography The effect of the addition of amino acids and amino acid derivatives on the crystallization of hemoglobin and ribonuclease A has been evaluated. The results showed that certain types of additives expand the concentration conditions in which crystals are formed. en PROTEIN CRYSTALLIZATION; PROMOTION OF CRYSTALLIZATION; ADDITIVES; AMINO ACIDS; AMINO ACID DERIVATIVES; PROTEIN AGGREGATION Determination of the appropriate conditions for protein crystallization remains a highly empirical process. Preventing protein aggregation is necessary for the formation of single crystals under aggregation-prone solution conditions. Because many amino acids and amino acid derivatives offer a unique combination of solubility and stabilizing properties, they open new avenues into the field of protein aggregation research. The use of amino acids and amino acid derivatives can potentially influence processes such as heat treatment and refolding reactions. The effect of the addition of several amino acids, such as lysine, and several amino acid derivatives, such as glycine ethyl ester and glycine amide, on the crystallization of equine hemoglobin and bovine pancreatic ribonuclease A has been examined. The addition of these amino acids and amino acid derivatives expanded the range of precipitant concentration in which crystals formed without aggregation. The addition of such additives appears to promote the crystallization of proteins. text/html Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 316 318 http://scripts.iucr.org/cgi-bin/paper?ys5013 Membrane-bound proteases are involved in various regulatory functions. A previous report indicates that the N-terminal region of PH1510 (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser–Lys dyad (Ser97 and Lys138), and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511. According to the crystal structure of the wild-type 1510-N in dimeric form, the active site around Ser97 is in a hydrophobic environment suitable for the hydrophobic substrates. This article reports the crystal structure of the K138A mutant of 1510-N at 2.3 Å resolution. The determined structure contains one molecule per asymmetric unit, but 1510-N is active in dimeric form. Two possible sets of dimer were found from the symmetry-related molecules. One dimer is almost the same as the wild-type 1510-N. Another dimer is probably in an inactive form. The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Yokoyama, H. Hamamatsu, S. Fujii, S. Matsui, I. 2008-05-01 doi:10.1107/S0909049507068471 International Union of Crystallography The crystal structure of the K138A mutant of the 1510-N protease specific for p-stomatin was determined at 2.3 Å resolution. The structure shows a novel dimer form, and the kinked L2 loop indicates that Lys138 would probably have an important effect on the conformation of L2. en MEMBRANE-BOUND PROTEASE; STOMATIN; CLPP; DIMERS; PYROCOCCUS HORIKOSHII Membrane-bound proteases are involved in various regulatory functions. A previous report indicates that the N-terminal region of PH1510 (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser–Lys dyad (Ser97 and Lys138), and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511. According to the crystal structure of the wild-type 1510-N in dimeric form, the active site around Ser97 is in a hydrophobic environment suitable for the hydrophobic substrates. This article reports the crystal structure of the K138A mutant of 1510-N at 2.3 Å resolution. The determined structure contains one molecule per asymmetric unit, but 1510-N is active in dimeric form. Two possible sets of dimer were found from the symmetry-related molecules. One dimer is almost the same as the wild-type 1510-N. Another dimer is probably in an inactive form. The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2. text/html Novel dimer structure of a membrane-bound protease with a catalytic Ser–Lys dyad and its linkage to stomatin text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 254 257 http://scripts.iucr.org/cgi-bin/paper?ys5030 BL-17A is a new structural biology beamline at the Photon Factory, Japan. The high-brilliance beam, derived from the new short-gap undulator (SGU#17), allows for unique protein crystallographic experiments such as data collection from microcrystals and structural determination using softer X-rays. However, microcrystal experiments require robust beam stability during data collection and minor fluctuations could not be ignored. Initially, significant beam instability was observed at BL-17A. The causes of the beam instability were investigated and its various sources identified. Subsequently, several effective countermeasures have been implemented, and the fluctuation of the beam intensity successfully suppressed to within 1%. Here the instability reduction techniques used at BL-17A are presented. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Igarashi, N. Ikuta, K. Miyoshi, T. Matsugaki, N. Yamada, Y. Yousef, M.S. Wakatsuki, S. 2008-05-01 doi:10.1107/S0909049507067118 International Union of Crystallography BL-17A is a new structural biology beamline at the Photon Factory, dedicated to protein crystallography of microcrystals. Here the X-ray beam stabilization techniques used at BL-17A are described. en PROTEIN MICROCRYSTALLOGRAPHY; PHOTON FACTORY; BEAMLINE DEVELOPMENT; X-RAY BEAM STABILIZATION BL-17A is a new structural biology beamline at the Photon Factory, Japan. The high-brilliance beam, derived from the new short-gap undulator (SGU#17), allows for unique protein crystallographic experiments such as data collection from microcrystals and structural determination using softer X-rays. However, microcrystal experiments require robust beam stability during data collection and minor fluctuations could not be ignored. Initially, significant beam instability was observed at BL-17A. The causes of the beam instability were investigated and its various sources identified. Subsequently, several effective countermeasures have been implemented, and the fluctuation of the beam intensity successfully suppressed to within 1%. Here the instability reduction techniques used at BL-17A are presented. text/html X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 292 295 http://scripts.iucr.org/cgi-bin/paper?ys5014 A prototype thermionic electron gun for a high-brightness X-ray generator has been developed. Its extraction voltage and design current are 60 kV and 100 mA (DC), respectively. The X-ray generator aims towards a maximum brilliance of 60 kW mm−2. The beam sizes at the rotating anticathode must therefore be within 1.0 mm × 0.1 mm and a small beam emittance is required. The fabricated electron gun optimizes an aperture grid and a Whenelt electrode. The performance of the prototype electron gun measured using pulsed-beam tests is as follows: maximum beam current, 85.7 mA; beam focus size at the rotating anticathode, 0.79 mm × 0.13 mm. In DC beam tests, FWHM beam sizes were measured to be 0.65 mm × 0.08 mm at the rotating anticathode with a beam current of 45 mA. The beam current recently reached ∼60 mA with some thermal problems. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Sugimura, T. Ohsawa, S. Ikeda, M. 2008-05-01 doi:10.1107/S0909049507066769 International Union of Crystallography The development of an electron gun for a high-brightness X-ray generator whose target brilliance is 60 kW mm−2 is reported. en ELECTRON GUN; DC BEAM; X-RAY GENERATOR A prototype thermionic electron gun for a high-brightness X-ray generator has been developed. Its extraction voltage and design current are 60 kV and 100 mA (DC), respectively. The X-ray generator aims towards a maximum brilliance of 60 kW mm−2. The beam sizes at the rotating anticathode must therefore be within 1.0 mm × 0.1 mm and a small beam emittance is required. The fabricated electron gun optimizes an aperture grid and a Whenelt electrode. The performance of the prototype electron gun measured using pulsed-beam tests is as follows: maximum beam current, 85.7 mA; beam focus size at the rotating anticathode, 0.79 mm × 0.13 mm. In DC beam tests, FWHM beam sizes were measured to be 0.65 mm × 0.08 mm at the rotating anticathode with a beam current of 45 mA. The beam current recently reached ∼60 mA with some thermal problems. text/html Performance of an electron gun for a high-brightness X-ray generator text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 258 261 http://scripts.iucr.org/cgi-bin/paper?me0358 Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 , 2008-01-01 doi:10.1107/S0909049507066332 International Union of Crystallography en text/html Current events text 1 15 2008-01-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography current events 111 114 http://scripts.iucr.org/cgi-bin/paper?ys5021 The bacterial envelope stress response, which is responsible for sensing stress signals in the envelope and for turning on the σE-dependent transcription, is modulated by the binding of RseB to RseA. In this study, the solution structures of RseA and its complex with RseB were analyzed using circular dichroism and small-angle X-ray scattering. The periplasmic domain of RseA is unstructured and flexible when it is not bound to RseB. However, upon the formation of the stable complex with RseB, RseA induces conformational changes in RseB and, at the same time, RseA becomes more structured. Furthermore, it appears that some other undefined region of RseA, as well as the previously identified minimum region (amino acid 169–186), is also involved in RseB binding. It is thought that these conformational changes are relevant to the proteolytic cleavage of RseA and the modulation of envelope stress response. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Jin, K.S. Kim, D.Y. Rho, Y. Le, V.B. Kwon, E. Kim, K.K. Ree, M. 2008-05-01 doi:10.1107/S0909049507066319 International Union of Crystallography Conformational changes of RseA and RseB were observed by circular dichroism and small-angle X-ray scattering upon the formation of their complex. en [SIGMA]E SIGNALING PATHWAY; ENVELOPE STRESS RESPONSE; RSEA; RSEB; SMALL-ANGLE X-RAY SCATTERING; CIRCULAR DICHROISM The bacterial envelope stress response, which is responsible for sensing stress signals in the envelope and for turning on the σE-dependent transcription, is modulated by the binding of RseB to RseA. In this study, the solution structures of RseA and its complex with RseB were analyzed using circular dichroism and small-angle X-ray scattering. The periplasmic domain of RseA is unstructured and flexible when it is not bound to RseB. However, upon the formation of the stable complex with RseB, RseA induces conformational changes in RseB and, at the same time, RseA becomes more structured. Furthermore, it appears that some other undefined region of RseA, as well as the previously identified minimum region (amino acid 169–186), is also involved in RseB binding. It is thought that these conformational changes are relevant to the proteolytic cleavage of RseA and the modulation of envelope stress response. text/html Solution structures of RseA and its complex with RseB text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 219 222 http://scripts.iucr.org/cgi-bin/paper?ys5005 Protein disulfide bond formation is catalyzed by a series of Dsb enzymes present in the periplasm of Escherichia coli. The crystal structure of the DsbB–DsbA–ubiquinone ternary complex provided important insights into mechanisms of the de novo disulfide bond generation cooperated by DsbB and ubiquinone and of the disulfide bond shuttle from DsbB to DsbA. The structural basis for prevention of the crosstalk between the DsbA–DsbB oxidative and the DsbC–DsbD reductive pathways has also been proposed. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Inaba, K. 2008-05-01 doi:10.1107/S090904950706061X International Union of Crystallography The crystal structure of the DsbB–DsbA–ubiquinone ternary complex has revealed a mechanism of protein disulfide bond generation in Escherichia coli. en PROTEIN DISULFIDE BOND GENERATION; ESCHERICHIA COLI Protein disulfide bond formation is catalyzed by a series of Dsb enzymes present in the periplasm of Escherichia coli. The crystal structure of the DsbB–DsbA–ubiquinone ternary complex provided important insights into mechanisms of the de novo disulfide bond generation cooperated by DsbB and ubiquinone and of the disulfide bond shuttle from DsbB to DsbA. The structural basis for prevention of the crosstalk between the DsbA–DsbB oxidative and the DsbC–DsbD reductive pathways has also been proposed. text/html Protein disulfide bond generation in Escherichia coli DsbB–DsbA text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 199 201 http://scripts.iucr.org/cgi-bin/paper?ys5032 There has been considerable interest recently in what is known as `fragment-based lead discovery'. The novel feature of the approach is to begin with small low-affinity compounds. The main advantage is that a larger potential chemical diversity can be sampled with fewer compounds, which is particularly important for new target classes. The approach relies on careful design of the fragment library, a method that can detect binding of the fragment to the protein target, determination of the structure of the fragment bound to the target, and the conventional use of structural information to guide compound optimization. In this article the methods are reviewed, and experiences in fragment-based discovery of lead series of compounds against kinases such as PDK1 and ATPases such as Hsp90 are discussed. The examples illustrate some of the key benefits and issues of the approach and also provide anecdotal examples of the patterns seen in selectivity and the binding mode of fragments across different protein targets. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Hubbard, R.E. 2008-05-01 doi:10.1107/S090904950705666X International Union of Crystallography Fragment-based methods are successfully generating novel and selective drug-like inhibitors of protein targets, with a number of groups reporting compounds entering clinical trials. This paper summarizes the key features of the approach as one of the tools in structure-guided drug discovery. en There has been considerable interest recently in what is known as `fragment-based lead discovery'. The novel feature of the approach is to begin with small low-affinity compounds. The main advantage is that a larger potential chemical diversity can be sampled with fewer compounds, which is particularly important for new target classes. The approach relies on careful design of the fragment library, a method that can detect binding of the fragment to the protein target, determination of the structure of the fragment bound to the target, and the conventional use of structural information to guide compound optimization. In this article the methods are reviewed, and experiences in fragment-based discovery of lead series of compounds against kinases such as PDK1 and ATPases such as Hsp90 are discussed. The examples illustrate some of the key benefits and issues of the approach and also provide anecdotal examples of the patterns seen in selectivity and the binding mode of fragments across different protein targets. text/html Fragment approaches in structure-based drug discovery text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 227 230 http://scripts.iucr.org/cgi-bin/paper?ys5015 Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The cA axis of domain A coincides with the cB axis of domain B with a smaller lattice, and the aA axis corresponds to the (aB + bB) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P41212 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Ohto, U. Satow, Y. 2008-05-01 doi:10.1107/S0909049507056531 International Union of Crystallography Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization. en CRYSTAL TWINNING; INNATE IMMUNITY; ENDOTOXIN Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The cA axis of domain A coincides with the cB axis of domain B with a smaller lattice, and the aA axis corresponds to the (aB + bB) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P41212 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method. text/html Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 262 265 http://scripts.iucr.org/cgi-bin/paper?ys5022 Studies of icosahedral virus capsids provide insights into the function of supramolecular machines. Virus capsid crystals have exceptionally large unit cells; as a result, they diffract weakly compared with protein crystals. HK97 is a dsDNA lambda-like bacteriophage whose 13 MDa capsid expands from 550 Å to 650 Å with large subunit conformational changes during virus maturation. The HK97 penultimate maturation intermediate was crystallized in a tetragonal unit cell that has lattice constants of 1010 Å × 1010 Å × 730 Å. The crystals could be cryoprotected, but diffracted to a modest resolution of 5 Å at a bending-magnet beamline. When these crystals were optimally exposed with two orders-of-magnitude more photons from a new insertion-device beamline, data extending to better than 3.8 Å resolution were obtained. Here, the strategies to collect and process such data are described. These strategies can be adapted for other crystals with large unit cells and for microcrystals. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Gan, L. Johnson, J.E. 2008-05-01 doi:10.1107/S0909049507064813 International Union of Crystallography Many supramolecular complexes form crystals that have lattice constants of the order of 1000 Å. An optimized method for data collection and processing is described. en VIRUS CRYSTALS; BACTERIOPHAGE HK97; INSERTION-DEVICE BEAMLINES Studies of icosahedral virus capsids provide insights into the function of supramolecular machines. Virus capsid crystals have exceptionally large unit cells; as a result, they diffract weakly compared with protein crystals. HK97 is a dsDNA lambda-like bacteriophage whose 13 MDa capsid expands from 550 Å to 650 Å with large subunit conformational changes during virus maturation. The HK97 penultimate maturation intermediate was crystallized in a tetragonal unit cell that has lattice constants of 1010 Å × 1010 Å × 730 Å. The crystals could be cryoprotected, but diffracted to a modest resolution of 5 Å at a bending-magnet beamline. When these crystals were optimally exposed with two orders-of-magnitude more photons from a new insertion-device beamline, data extending to better than 3.8 Å resolution were obtained. Here, the strategies to collect and process such data are described. These strategies can be adapted for other crystals with large unit cells and for microcrystals. text/html An optimal exposure strategy for cryoprotected virus crystals with lattice constants greater than 1000 Å text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 223 226 http://scripts.iucr.org/cgi-bin/paper?ys5028 A mail-in data collection system makes it possible for beamline users to collect diffraction data without visiting a synchrotron facility. In the mail-in data collection system at SPring-8, users pack crystals into sample trays and send the trays to SPring-8 via a courier service as the first step. Next, the user specifies measurement conditions and checks the diffraction images via the Internet. The user can also collect diffraction data using an automated sample changer robot and beamline control software. For distant users there is a newly developed data management system, D-Cha. D-Cha provides a graphical user interface that enables the user to specify the experimental conditions for samples and to check and download the diffraction images using a web browser. This system is now in routine operation and is contributing to high-throughput beamline operation. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Okazaki, N. Hasegawa, K. Ueno, G. Murakami, H. Kumasaka, T. Yamamoto, M. 2008-05-01 doi:10.1107/S0909049507064679 International Union of Crystallography A mail-in data collection system at SPring-8, which is a web application with automated beamline operation, has been developed. en MAIL-IN DATA COLLECTION; HIGH-THROUGHPUT DATA COLLECTION; BEAMLINE AUTOMATION; WEB APPLICATION; DATABASE SYSTEM A mail-in data collection system makes it possible for beamline users to collect diffraction data without visiting a synchrotron facility. In the mail-in data collection system at SPring-8, users pack crystals into sample trays and send the trays to SPring-8 via a courier service as the first step. Next, the user specifies measurement conditions and checks the diffraction images via the Internet. The user can also collect diffraction data using an automated sample changer robot and beamline control software. For distant users there is a newly developed data management system, D-Cha. D-Cha provides a graphical user interface that enables the user to specify the experimental conditions for samples and to check and download the diffraction images using a web browser. This system is now in routine operation and is contributing to high-throughput beamline operation. text/html Mail-in data collection at SPring-8 protein crystallography beamlines text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 288 291 http://scripts.iucr.org/cgi-bin/paper?ys5033 Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10 s. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Hiraki, M. Watanabe, S. pHonda, N. Yamada, Y. Matsugaki, N. Igarashi, N. Gaponov, Y. Wakatsuki, S. 2008-05-01 doi:10.1107/S0909049507064680 International Union of Crystallography Sample-exchange robots with a double-tongs system that could exchange samples within 10 s have been developed. en SAMPLE-EXCHANGE ROBOT; PROTEIN CRYSTALLOGRAPHY; AUTOMATED SYSTEM; DIFFRACTION EXPERIMENT Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10 s. text/html High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 300 303 http://scripts.iucr.org/cgi-bin/paper?ys5010 d-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Ω loop, and a ground state with a disordered Ω loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oη, Ser60 Oγ and Lys63 Nζ revealed that Tyr149 Oη donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oη donates an H atom to Ser60 Oγ or Lys63 Nζ in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oη, Ser60 Oγ and Lys63 Nζ, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oη in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Okazaki, S. Suzuki, A. Komeda, H. Asano, Y. Yamane, T. 2008-05-01 doi:10.1107/S0909049507064655 International Union of Crystallography The catalytic mechanism of d-amino acid amidase from Ochrobactrum anthropi SV3 has been deduced. en CATALYTIC MECHANISMS; STEREOSPECIFIC HYDROLYSIS; D-AMINO ACID AMIDASE d-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Ω loop, and a ground state with a disordered Ω loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oη, Ser60 Oγ and Lys63 Nζ revealed that Tyr149 Oη donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oη donates an H atom to Ser60 Oγ or Lys63 Nζ in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oη, Ser60 Oγ and Lys63 Nζ, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oη in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. text/html Deduced catalytic mechanism of d-amino acid amidase from Ochrobactrum anthropi SV3 text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 250 253 http://scripts.iucr.org/cgi-bin/paper?ys5008 The structures of both native and S139A holo-HCV NS3/4A protease domain were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in complex with the protease. The changes in the inhibitor potency were correlated with changes in the buried surface area upon binding the inhibitor to the active site. The largest contributions to the binding energy arise from the hydrophobic interactions of the P1 and P2 groups as they bind to the S1 and S2 pockets. This correlation of the changes in potency with increased buried surface area contributed directly to the design of a potent tripeptide inhibitor of the HCV NS3/4A protease, which is currently in clinical trials. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Madison, V. Prongay, A.J. Guo, Z. Yao, N. Pichardo, J. Fischmann, T. Strickland, C. Myers Jr, J. Weber, P.C. Beyer, B.M. Ingram, R. Hong, Z. Prosise, W.W. Ramanathan, L. Taremi, S.S. Yarosh-Tomaine, T. Zhang, R. Senior, M. Yang, R.-S. Malcolm, B. Arasappan, A. Bennett, F. Bogen, S.L. Chen, K. Jao, E. Liu, Y.-T. Lovey, R.G. Saksena, A.K. Venkatraman, S. Girijavallabhan, V. Njoroge, F.G. 2008-05-01 doi:10.1107/S0909049507064229 International Union of Crystallography Crystal structures of protease/inhibitor complexes guided optimization of the buried nonpolar surface area thereby maximizing hydrophobic binding. The resulting potent tripeptide inhibitor is in clinical trials. en HCV PROTEASE; STRUCTURE-BASED DESIGN; KETOAMIDES; HYDROPHOBIC BINDING The structures of both native and S139A holo-HCV NS3/4A protease domain were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in complex with the protease. The changes in the inhibitor potency were correlated with changes in the buried surface area upon binding the inhibitor to the active site. The largest contributions to the binding energy arise from the hydrophobic interactions of the P1 and P2 groups as they bind to the S1 and S2 pockets. This correlation of the changes in potency with increased buried surface area contributed directly to the design of a potent tripeptide inhibitor of the HCV NS3/4A protease, which is currently in clinical trials. text/html Key steps in the structure-based optimization of the hepatitis C virus NS3/4A protease inhibitor SCH503034 text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 204 207 http://scripts.iucr.org/cgi-bin/paper?ys5009 The degradation of ssrA-tagged substrates in prokaryotes is conducted by a subset of ATP-dependent proteases, including ClpXP complex. More than 630 sequences of ssrA have been identified from 514 species, and are conserved in a wide range of prokaryotes. SspB protein markedly stimulates the degradation of these ssrA-tagged substrates by the ClpXP proteolytic machine. The dimeric SspB protein is composed of a compact ssrA-binding domain, which has a dimerization surface and a flexible C-terminal tail with a ClpX-binding motif at its very end. Since SspB is an adaptor protein for the ClpXP complex, designed mutagenesis, fluorescence spectroscopy, biochemistry and X-ray crystallography have been used to investigate the mechanism of delivery of ssrA-tagged proteins. In this paper the structural basis of ssrA-tag recognition by ClpX and SspB, as well as SspB-tail recognition by ZBD, is described. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Park, E.Y. Song, H.K. 2008-05-01 doi:10.1107/S0909049507062826 International Union of Crystallography Substrates tagged with ssrA are recognized and degraded by a subset of the Clp family, ATP-dependent proteases in prokaryotes. This paper describes the mechanism of intracellular breakdown of ssrA-tagged substrates by ClpXP and its adaptor protein, SspB. en ADAPTOR; CLPX; CLPXP COMPLEX; SSPB; SSRA; ZINC-BINDING DOMAIN The degradation of ssrA-tagged substrates in prokaryotes is conducted by a subset of ATP-dependent proteases, including ClpXP complex. More than 630 sequences of ssrA have been identified from 514 species, and are conserved in a wide range of prokaryotes. SspB protein markedly stimulates the degradation of these ssrA-tagged substrates by the ClpXP proteolytic machine. The dimeric SspB protein is composed of a compact ssrA-binding domain, which has a dimerization surface and a flexible C-terminal tail with a ClpX-binding motif at its very end. Since SspB is an adaptor protein for the ClpXP complex, designed mutagenesis, fluorescence spectroscopy, biochemistry and X-ray crystallography have been used to investigate the mechanism of delivery of ssrA-tagged proteins. In this paper the structural basis of ssrA-tag recognition by ClpX and SspB, as well as SspB-tail recognition by ZBD, is described. text/html A degradation signal recognition in prokaryotes text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 246 249 http://scripts.iucr.org/cgi-bin/paper?ys5035 SLPI (secretory leukocyte protease inhibitor) is a 107-residue non-glycosylated protease inhibitor, which inhibits a wide range of serine proteases, trypsin, chymotrypsin, neutrophil elastase, chymase and cathepsin G. X-ray crystallographic analyses have shown that SLPI comprises two separate domains of similar architecture [Grütter, Fendrich, Huber & Bode (1988), EMBO J. 7, 345–351] and the C-terminal domain interacts with bovine α-chymotrypsin. In order to understand SLPI's multiple functions against various serine proteases, the complex HNE (human neutrophil elastase) has been co-crystallized with 1/2SLPI (recombinant C-terminal domain of SLPI; Arg58–Ala107), which has a biological activity similar to full SLPI. The 1/2SLPI and HNE complex structure was solved at 1.7 Å resolution, and compared with the interaction mechanism of elafin, which is a specific inhibitor of elastase. It was found that P1 Leu72i and six hydrogen bonds between the main chains in the primary contact region have sufficient ability to inhibit HNE and PPE (porcine pancreatic elastase), and P5 Tyr68i is important in increasing the selectivity of 1/2SLPI against HNE. The mechanisms of the functions of SLPI are relatively unknown, but the current study could help understand the selectivity of SLPI against HNE and PPE. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Koizumi, M. Fujino, A. Fukushima, K. Kamimura, T. Takimoto-Kamimura, M. 2008-05-01 doi:10.1107/S0909049507060670 International Union of Crystallography The 1/2SLPI and HNE complex structure was solved at 1.7 Å resolution and compared with the interaction mechanism of elafin. en ELASTASE INHIBITOR; CRYSTAL STRUCTURE; SLPI SLPI (secretory leukocyte protease inhibitor) is a 107-residue non-glycosylated protease inhibitor, which inhibits a wide range of serine proteases, trypsin, chymotrypsin, neutrophil elastase, chymase and cathepsin G. X-ray crystallographic analyses have shown that SLPI comprises two separate domains of similar architecture [Grütter, Fendrich, Huber & Bode (1988), EMBO J. 7, 345–351] and the C-terminal domain interacts with bovine α-chymotrypsin. In order to understand SLPI's multiple functions against various serine proteases, the complex HNE (human neutrophil elastase) has been co-crystallized with 1/2SLPI (recombinant C-terminal domain of SLPI; Arg58–Ala107), which has a biological activity similar to full SLPI. The 1/2SLPI and HNE complex structure was solved at 1.7 Å resolution, and compared with the interaction mechanism of elafin, which is a specific inhibitor of elastase. It was found that P1 Leu72i and six hydrogen bonds between the main chains in the primary contact region have sufficient ability to inhibit HNE and PPE (porcine pancreatic elastase), and P5 Tyr68i is important in increasing the selectivity of 1/2SLPI against HNE. The mechanisms of the functions of SLPI are relatively unknown, but the current study could help understand the selectivity of SLPI against HNE and PPE. text/html Complex of human neutrophil elastase with 1/2SLPI text 3 15 2008-05-01 Journal of Synchrotron Radiation Copyright (c) 2008 International Union of Crystallography short communications 308 311 http://scripts.iucr.org/cgi-bin/paper?ys5037 To observe the ionized status of the amino acid residues in proteins at different pH (protein pH titration in the crystalline state) by neutron diffraction, hen egg-white lysozyme was crystallized over a wide pH range (2.5–8.0). Crystallization phase diagrams at pH 2.5, 6.0 and 7.5 were determined. At pH < 4.5 the border between the metastable region and the nucleation region shifted to the left (lower precipitant concentration) in the phase diagram, and at pH > 4.5 the border shifted to the right (higher precipitant concentration). The qualities of these crystals were characterized using the Wilson plot method. The qualities of all crystals at different pH were more or less equivalent (B-factor values within 25–40). It is expected that neutron diffraction analysis of these crystals of different pH provides equivalent data in quality for discussions of protein pH titration in the crystalline state of hen egg-white lysozyme. Copyright (c) 2008 International Union of Crystallography urn:issn:0909-0495 Iwai, W. Yagi, D. Ishikawa, T. Ohnishi, Y. Tanaka, I. Niimura, N. 2008-05-01 doi:10.1107/S0909049507059559 International Union of Crystallography