Acta Crystallographica Section D

Biological Crystallography

Volume 61, Part 6 (June 2005)


Proceedings of the 10th International Conference on the Crystallization of Biological Macromolecules

Beijing, People's Republic of China, 5-8 June 2004

[Buy print version] A printed copy of this issue is available for purchase

[Preface]
[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: ICCBM10

crystallization for structural genomics


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Acta Cryst. (2005). D61, 651-657  [ doi:10.1107/S0907444905007808 ]

A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization

T. S. Walter, J. M. Diprose, C. J. Mayo, C. Siebold, M. G. Pickford, L. Carter, G. C. Sutton, N. S. Berrow, J. Brown, I. M. Berry, G. B. E. Stewart-Jones, J. M. Grimes, D. K. Stammers, R. M. Esnouf, E. Y. Jones, R. J. Owens, D. I. Stuart and K. Harlos

Synopsis: The current workflow for crystallization at the Oxford Protein Production Facility (OPPF) is described.

Online 26 May 2005


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Acta Cryst. (2005). D61, 658-663  [ doi:10.1107/S090744490500939X ]

Development of a fully automated macromolecular crystallization/observation robotic system, HTS-80

H. Miyatake, S.-H. Kim, I. Motegi, H. Matsuzaki, H. Kitahara, A. Higuchi and K. Miki

Synopsis: A fully automated robotic system for the crystallization and observation of macromolecules, HTS-80, has been developed.

Online 26 May 2005


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Acta Cryst. (2005). D61, 664-670  [ doi:10.1107/S0907444905000028 ]

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

N. Leulliot, L. Trésaugues, M. Bremang, I. Sorel, N. Ulryck, M. Graille, I. Aboulfath, A. Poupon, D. Liger, S. Quevillon-Cheruel, J. Janin and H. van Tilbeurgh

Synopsis: Discussion of high-throughput optimization strategies used in the Yeast Structural Genomics Project, with selected successful examples.

Online 26 May 2005


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Acta Cryst. (2005). D61, 671-678  [ doi:10.1107/S0907444905001290 ]

HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories

J. Prilusky, E. Oueillet, N. Ulryck, A. Pajon, J. Bernauer, I. Krimm, S. Quevillon-Cheruel, N. Leulliot, M. Graille, D. Liger, L. Trésaugues, J. L. Sussman, J. Janin, H. van Tilbeurgh and A. Poupon

Synopsis: HalX, software designed as an `electronic lab book', aims at (i) storage and (ii) easy access and use of all experimental data. Its use should lead to much improved management and tracking of structural genomics experimental data.

Online 26 May 2005


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Acta Cryst. (2005). D61, 679-684  [ doi:10.1107/S0907444905013132 ]

The high-throughput protein-to-structure pipeline at SECSG

Z.-J. Liu, W. Tempel, J. D. Ng, D. Lin, A. K. Shah, L. Chen, P. S. Horanyi, J. E. Habel, I. A. Kataeva, H. Xu, H. Yang, J. C. Chang, L. Huang, S.-H. Chang, W. Zhou, D. Lee, J. L. Praissman, H. Zhang, M. G. Newton, J. P. Rose, J. S. Richardson, D. C. Richardson and B.-C. Wang

Synopsis: The high-throughput crystal structure determination pipeline at Southeast Collaboratory for Structural Genomics, a pilot center of the National Institutes of Health Protein Structure Initiative, is described.

Online 26 May 2005


obtaining the first crystals


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Acta Cryst. (2005). D61, 685-689  [ doi:10.1107/S0907444904028707 ]

Crystallization and crystal manipulation of the Pterocarpus angolensis seed lectin

R. Loris, A. Garcia-Pino, L. Buts, J. Bouckaert, S. Beeckmans, H. De Greve and L. Wyns

Synopsis: The Man/Glc-specific lectin from P. angolensis was crystallized in complex with Man([alpha]1-3)ManMe. Competition soaks allowed the replacement of the bound disaccharide by a series of different mono- and oligosaccarides, as well as extraction of the bound sugar and metal ions.

Online 26 May 2005


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Acta Cryst. (2005). D61, 690-693  [ doi:10.1107/S0907444904029348 ]

Crystallization and preliminary X-ray analysis of strictosidine synthase and its complex with the substrate tryptamine

J. Koepke, X. Ma, G. Fritzsch, H. Michel and J. Stöckigt

Synopsis: Strictosidine synthase is a central enzyme that participates in the biosynthesis of plant monoterpenoid indole alkaloids. The native enzyme and its complex with the substrate tryptamine were crystallized and analyzed by X-rays.

Online 26 May 2005


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Acta Cryst. (2005). D61, 694-696  [ doi:10.1107/S0907444904028756 ]

Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina

X. Ma, J. Koepke, A. Bayer, G. Fritzsch, H. Michel and J. Stöckigt

Synopsis: Crystals of vinorine synthase and selenomethionyl-labelled vinorine synthase have been obtained by a hanging-drop method and were analyzed by X-ray crystallography. Vinorine synthase is the first crystallized enzyme which belongs to the BAHD superfamily.

Online 26 May 2005


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Acta Cryst. (2005). D61, 697-700  [ doi:10.1107/S0907444905014174 ]

Crystallization of soluble urokinase receptor (suPAR) in complex with urokinase amino-terminal fragment (1-143)

M. Huang, A. P. Mazar, G. Parry, A.A.-R. Higazi, A. Kuo and D. B. Cines

Synopsis: Crystallization of a suPAR-ATF complex.

Online 26 May 2005


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Acta Cryst. (2005). D61, 701-703  [ doi:10.1107/S0907444904034432 ]

Crystallization of an anti-factor IX antibody and its complex

X. Shi, Y. Li, C. Bian, G. Zhao and M. Huang

Synopsis: Crystallization of an anti-factor IX antibody.

Online 26 May 2005


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Acta Cryst. (2005). D61, 704-709  [ doi:10.1107/S0907444905006761 ]

Crystallization of canavalin as a function of pH

E. L. Forsythe, S. Gorti and M. L. Pusey

Synopsis: Canavalin is found to crystallize from pH 6.4 to 9.6. Fluorescence anisotropy and light-scattering measurements indicate that the solution is composed of trimers.

Online 26 May 2005


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Acta Cryst. (2005). D61, 710-712  [ doi:10.1107/S0907444905006864 ]

Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl

M. Kamo, K. Inouye, K. Nagata and M. Tanokura

Synopsis: This report details a new method to introduce high concentrations of NaCl into crystals of thermolysin. The crystal obtained by this method diffracted X-rays to 2.43 Å and the crystal structure of thermolysin in the presence of 4 M NaCl was solved for the first time.

Online 26 May 2005


preparation of complex biomacromolecules


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Acta Cryst. (2005). D61, 713-719  [ doi:10.1107/S0907444905006311 ]

Reproducible growth of well diffracting ribosomal crystals

T. Auerbach-Nevo, R. Zarivach, M. Peretz and A. Yonath

Synopsis: The crystal quality of the large ribosomal subunit was enhanced using active-state ribosomes.

Online 26 May 2005


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Acta Cryst. (2005). D61, 720-723  [ doi:10.1107/S0907444904030756 ]

The incorporation of large impurities into virus crystals

Yu. G. Kuznetsov, D. L. Makino, A. J. Malkin and A. McPherson

Synopsis: Virus crystals can incorporate a wide range of unusual impurities, not possible for conventional crystals or even most protein crystals, because of the large size of their constituent particles. Examples of several of these unusual impurities are presented here, along with some of the consequences for the crystal lattices.

Online 26 May 2005


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Acta Cryst. (2005). D61, 724-730  [ doi:10.1107/S0907444904029063 ]

The role of protein and surfactant interactions in membrane-protein crystallization

B. W. Berger, C. M. Gendron, C. R. Robinson, E. W. Kaler and A. M. Lenhoff

Synopsis: Interactions leading to crystallization of the integral membrane protein bacteriorhodopsin were investigated. Osmotic second virial coefficients were measured by self-interaction chromatography.

Online 26 May 2005


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Acta Cryst. (2005). D61, 731-736  [ doi:10.1107/S0907444905009595 ]

Structure determination of GGA-GAE and [gamma]1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic

Y. Yamada, M. Inoue, T. Shiba, M. Kawasaki, R. Kato, K. Nakayama and S. Wakatsuki

Synopsis: Crystal structures of GGA1-GAE and [gamma]1-ear domains in complex with cognate peptides were determined. Use of peptide-tagged proteins for crystallization of the [gamma]1-ear/peptide complexes improved the diffraction qualities significantly.

Online 26 May 2005


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Acta Cryst. (2005). D61, 737-743  [ doi:10.1107/S0907444905000053 ]

The mechanism of high-pressure-induced ordering in a macromolecular crystal

T. Lin, W. Schildkamp, K. Brister, P. C. Doerschuk, M. Somayazulu, H. Mao and J. E. Johnson

Synopsis: A mechanistic model consistent with experimental data is proposed for the pressure-induced ordering of a macromolecular crystal.

Online 26 May 2005


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Acta Cryst. (2005). D61, 744-749  [ doi:10.1107/S0907444905006724 ]

Different crystal packing in Fab-protein L semi-disordered peptide complex

R. Ménez, N. G. Housden, S. Harrison, C. Jolivet-Reynaud, M. G. Gore and E. A. Stura

Synopsis: Peptides whose conformation is ill defined can be crystallized in complex with proteins where in the lattice they will adopt multiple conformations. The peptide in complex with an anti-HCV monoclonal antibody is most ordered where it has the most space to achieve it own energy minimum.

Online 26 May 2005


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Acta Cryst. (2005). D61, 750-754  [ doi:10.1107/S0907444905007110 ]

Comparison of the crystallization and crystal packing of two Fab single-site mutant protein L complexes

V. Granata, N. G. Housden, S. Harrison, C. Jolivet-Reynaud, M. G. Gore and E. A. Stura

Synopsis: Tryptophans introduced in protein L (PpL) for stopped-flow fluorescence studies make crystal contacts when two different PpL mutants, Y64W and A66W are crystallized bound to an Fab'. The lattice parameters are almost identical in two crystallographic directions, but are significantly different in the third direction, showing that a small displacement of a contact residue is amplified in the lattice.

Online 26 May 2005


improving crystal and data qualities


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Acta Cryst. (2005). D61, 755-758  [ doi:10.1107/S0907444905000405 ]

Investigation of the protein pre-crystallization solution using analytical ultracentrifugation

I. Yoshizaki, M. Sakai and Y. Matsuura

Synopsis: Analytical ultracentrifugation was used to study the crystal growth units in hen egg-white lysozyme pre-crystallization solution.

Online 26 May 2005


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Acta Cryst. (2005). D61, 759-762  [ doi:10.1107/S0907444905013466 ]

Solution stirring initiates nucleation and improves the quality of adenosine deaminase crystals

H. Adachi, K. Takano, A. Niino, H. Matsumura, T. Kinoshita, M. Warizaya, T. Inoue, Y. Mori and T. Sasaki

Synopsis: A solution-stirring technique was used to obtain high-quality ADA complex and ADA native crystals.

Online 26 May 2005


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Acta Cryst. (2005). D61, 763-771  [ doi:10.1107/S0907444904028902 ]

Extracting trends from two decades of microgravity macromolecular crystallization history

R. A. Judge, E. H. Snell and M. J. van der Woerd

Synopsis: Trends were analyzed from two decades of microgravity crystallization history. It was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission.

Online 26 May 2005


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Acta Cryst. (2005). D61, 772-775  [ doi:10.1107/S0907444904028768 ]

Optimizing protein crystal growth through dynamic seeding

D.-Y. Zhu, Y.-Q. Zhu, Y. Xiang and D.-C. Wang

Synopsis: A dynamic seeding method different from the conventional methods in a non-equilibrium serial micro/macroseeding and its successful use in the optimization of the CutCm protein crystal growth are described.

Online 26 May 2005


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Acta Cryst. (2005). D61, 776-779  [ doi:10.1107/S0907444905014708 ]

An attempt to increase the efficiency of protein crystal screening: a simplified screen and experiments

W. Gao, S. Li and R. Bi

Synopsis: A simplified screen has been designed based on the efficiency of crystallization conditions from different screens and relevant studies and results of test experiments have shown that it could improve the success rate of crystallization and reduce consumption.

Online 26 May 2005


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Acta Cryst. (2005). D61, 780-783  [ doi:10.1107/S0907444904034407 ]

Anaerobic purification and crystallization to improve the crystal quality: ferredoxin II from Desulfovibrio gigas

Y.-C. Hsieh, M.-Y. Liu, J. Le Gall and C.-J. Chen

Synopsis: Anaerobic crystallization of ferredoxin II from D. gigas.

Online 26 May 2005


 

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Acta Cryst. (2005). D61, 784-788  [ doi:10.1107/S0907444905007109 ]

Crystal quality and differential crystal-growth behaviour of three proteins crystallized in gel at high hydrostatic pressure

A. Kadri, B. Lorber, C. Charron, M.-C. Robert, B. Capelle, M. Damak, G. Jenner and R. Giegé

Synopsis: Crystallization under pressure and in agarose gel of thaumatin and two lysozymes reveals specific effects that are correlated with alterations of the protein hydration shells.

Online 26 May 2005


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Acta Cryst. (2005). D61, 789-792  [ doi:10.1107/S0907444905007122 ]

Effects of macromolecular impurities and of crystallization method on the quality of eubacterial aspartyl-tRNA synthetase crystals

A. Moreno, A. Théobald-Dietrich, B. Lorber, C. Sauter and R. Giegé

Synopsis: Minute amounts of protein impurities alter the growth of aspartyl-tRNA synthetase crystals. With the purest enzyme, the best crystals are grown in environments where convection is reduced.

Online 26 May 2005


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Acta Cryst. (2005). D61, 793-798  [ doi:10.1107/S0907444905001368 ]

Protein crystal perfection and its application

J. R. Helliwell

Synopsis: The assessment of protein crystal perfection with X-rays is reviewed. Several X-ray diffraction physics applications with protein crystals that harness perfection are given. Applications in neutron protein crystallography are then described.

Online 26 May 2005


new approaches


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Acta Cryst. (2005). D61, 799-802  [ doi:10.1107/S0907444905008085 ]

Development of a novel ampholyte buffer for isoelectric focusing: electric charge-separation of protein samples for X-ray crystallography using free-flow isoelectric focusing

S.-H. Kim, H. Miyatake, T. Ueno, T. Nagao and K. Miki

Synopsis: A novel ampholyte buffer suitable for crystallization using the ProTeam FFE apparatus has been developed. This buffer is able to generate pH gradients owing to the use of low-molecular-weight electrolytes.

Online 26 May 2005


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Acta Cryst. (2005). D61, 803-808  [ doi:10.1107/S0907444905006578 ]

Comparison of lysozyme structures derived from thin-film-based and classical crystals

E. Pechkova, V. Sivozhelezov, G. Tropiano, S. Fiordoro and C. Nicolini

Synopsis: A report of the systematic comparison of crystal structures produced by the nanobiofilm template method and by the classical hanging-drop vapour-diffusion method.

Online 26 May 2005


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Acta Cryst. (2005). D61, 809-812  [ doi:10.1107/S0907444905006566 ]

Investigating crystal-growth mechanisms with and without LB template: protein transfer from LB to crystal

E. Pechkova, S. Fiordoro, D. Fontani and C. Nicolini

Synopsis: In lysozyme crystal growth induced by a lysozyme thin-film template direct protein transfer appears to occur from the LB film into the crystal being formed, giving a possible explanation for the mechanisms involved in crystal nucleation and growth.

Online 26 May 2005


crystal growth physics


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Acta Cryst. (2005). D61, 813-818  [ doi:10.1107/S0907444905006943 ]

Supersaturated lysozyme solution structure studied by chemical cross-linking

C. L. Hall, J. R. Clemens, A. M. Brown and L. J. Wilson

Synopsis: Glutaraldehyde cross-linking followed by separation has been used to detect aggregates of chicken egg-white lysozyme (CEWL) in supersaturated solutions

Online 26 May 2005


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Acta Cryst. (2005). D61, 819-825  [ doi:10.1107/S090744490402949X ]

Quantitative imaging by confocal scanning fluorescence microscopy of protein crystallization via liquid-liquid phase separation

D. Vivarès, E. W. Kaler and A. M. Lenhoff

Synopsis: Metastable states such as liquid-liquid phase separation, aggregation and gelation can affect protein crystallization. Mixtures of PEG and a large model protein, glucose isomerase, have been studied to characterize the effect of a metastable liquid-liquid phase separation on protein crystallization.

Online 26 May 2005


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Acta Cryst. (2005). D61, 826-831  [ doi:10.1107/S0907444905013703 ]

Surface morphology and kinetic properties in rapid growth of EAFP protein crystals investigated by atomic force microscopy

S. Wang, G. Li, Y. Xiang, R.-H. Huang, Y. Zhang and D.-C. Wang

Synopsis: The surface morphology and kinetic properties of rapid growth of EAFP protein crystals are observed by atomic force microscopy. The characteristic pattern related to the rapid growth is discussed.

Online 26 May 2005


 

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Acta Cryst. (2005). D61, 832-836  [ doi:10.1107/S0907444905013569 ]

van der Waals phase transition in protein solutions

P. R. Wills and D. J. Winzor

Synopsis: The van der Waals equation of state for imperfect gases is applied to solutions of macromolecules, especially to explain the fluid-fluid phase transition in protein solutions. Due account is taken of dimerization owing to intermolecular attraction, hard-sphere and electrostatic repulsion, as well as excluded volume effects caused by inert co-solutes.

Online 26 May 2005


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Acta Cryst. (2005). D61, 837-843  [ doi:10.1107/S0907444905006487 ]

Measurable characteristics of lysozyme crystal growth

S. Gorti, E. L. Forsythe and M. L. Pusey

Synopsis: Physical processes that effect protein crystal growth velocities are discussed. In particular, methods that can be applied to determine the occurrence of kinetic roughening are evaluated.

Online 26 May 2005


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