Acta Crystallographica Section D

Biological Crystallography

Volume 59, Part 1 (January 2003)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: A representation of the fold of yeast hypothetical protein with PLP and protein ligand Lys49 which is bound to PLP (p. 127).

editorial


 

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Acta Cryst. (2003). D59, 1  [ doi:10.1107/S090744490202245X ]

Changing of the guard

E. N. Baker and Z. Dauter

Online 20 December 2002


topical reviews


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Acta Cryst. (2003). D59, 2-15  [ doi:10.1107/S0907444902021443 ]

Physical aspects of protein crystal growth investigated with the Advanced Protein Crystallization Facility in reduced-gravity environments

A. Vergara, B. Lorber, A. Zagari and R. Giegé

Synopsis: Physicochemical insights into protein crystallization investigated with the Advanced Protein Crystallization Facility are critically reviewed.

Online 20 December 2002


research papers


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Acta Cryst. (2003). D59, 16-22  [ doi:10.1107/S0907444902017523 ]

Structure of the N-terminal domain of human FKBP52

P. Li, Y. Ding, B. Wu, C. Shu, B. Shen and Z. Rao

Synopsis: The structure of the N-terminal domain of human FKBP52 was determined using molecular replacement to 2.4 Å. The overall structure is very similar to FKBP12, and the structure-functional relationship of the protein is discussed.

PDB reference: 1n1a

Online 20 December 2002


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Acta Cryst. (2003). D59, 23-31  [ doi:10.1107/S0907444902017705 ]

Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis

H. Kishida, T. Wada, S. Unzai, T. Kuzuyama, M. Takagi, T. Terada, M. Shirouzu, S. Yokoyama, J. R. H. Tame and S.-Y. Park

Synopsis: The structure of an enzyme involved in the non-mevalonate pathway of isoprenoid synthesis in the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue.

PDB references: 1iv1, 1iv2, 1iv3 and 1iv4

Online 20 December 2002


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Acta Cryst. (2003). D59, 32-37  [ doi:10.1107/S0907444902018000 ]

Is the bond-valence method able to identify metal atoms in protein structures?

P. Müller, S. Köpke and G. M. Sheldrick

Synopsis: The calcium bond-valence sum (CBVS) is proposed as a convenient way of identifying metal ions in protein structures.

Online 20 December 2002


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Acta Cryst. (2003). D59, 38-44  [ doi:10.1107/S0907444902018036 ]

Automated main-chain model building by template matching and iterative fragment extension

T. C. Terwilliger

Synopsis: A method for automated macromolecular main-chain model building is described.

Online 20 December 2002


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Acta Cryst. (2003). D59, 45-49  [ doi:10.1107/S0907444902018048 ]

Automated side-chain model building and sequence assignment by template matching

T. C. Terwilliger

Synopsis: A method for automated macromolecular side-chain model building and for aligning the sequence to the map is described.

Online 20 December 2002


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Acta Cryst. (2003). D59, 50-56  [ doi:10.1107/S0907444902018851 ]

Three-dimensional structure of homodimeric cholesterol esterase-ligand complex at 1.4 Å resolution

V. Pletnev, A. Addlagatta, Z. Wawrzak and W. Duax

Synopsis: The 1.4 Å resolution three-dimensional structure of a homodimeric cholesterol esterase (Candida cylindracea) in complex with an unknown ligand revealed the presence of a C23-chain fatty acid in an elongated enzyme active site.

PDB reference: 1llf

Online 20 December 2002


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Acta Cryst. (2003). D59, 57-66  [ doi:10.1107/S090744490201884X ]

Locating the anomalous scatterer substructures in halide and sulfur phasing

I. Usón, B. Schmidt, R. von Bülow, S. Grimme, K. von Figura, M. Dauter, K. R. Rajashankar, Z. Dauter and G. M. Sheldrick

Synopsis: The phasing of proteins using the anomalous signal from inherent sulfur or halides in the solvent requires the coordinates of an appreciable number of partially occupied or weak sites to be determined. The use of dual-space recycling methods, as implemented in the program SHELXD, to solve such anomalous scatterer substructures in MAD, SAD, SIR and SIRAS experiments has been tested on a previously unknown protein structure.

PDB references: 1e6f and 1gqb

Online 20 December 2002


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Acta Cryst. (2003). D59, 67-72  [ doi:10.1107/S0907444902018917 ]

Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA

B. Ramakrishnan, C. Sekharudu, B. Pan and M. Sundaralingam

Synopsis: An A-DNA decamer at 1.25 Å resolution shows a novel binding mode of cobalt hexammine ion to DNA duplexes. Analysis of thermal parameters (B factors) indicates that nucleotides involved in abutting crystal packing are thermally more stable than other nucleotdes in the duplex.

PDB reference: 1m77

NDB reference: ad0026

Online 20 December 2002


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Acta Cryst. (2003). D59, 73-76  [ doi:10.1107/S0907444902018929 ]

Structure of Escherichia coli uridine phosphorylase at 2.0 Å

F. T. Burling, R. Kniewel, J. A. Buglino, T. Chadha, A. Beckwith and C. D. Lima

Synopsis: The 2.0 Å resolution crystal structure of E. coli uridine phosphorylase suggests greater structural similarity to E. coli purine phosphorylase, lending further support to the hypothesis that members of the related but functionally distinct NP-I enzyme class evolved from a common ancestor.

PDB reference: 1lx7

Online 20 December 2002


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Acta Cryst. (2003). D59, 77-83  [ doi:10.1107/S0907444902019236 ]

A rapid method for assessing lipid:protein and detergent:protein ratios in membrane-protein crystallization

C. J. B. daCosta and J. E. Baenziger

Synopsis: A simple rapid method using infrared spectroscopy for measuring lipid:protein ratios and detergent concentrations in solubilized integral membrane-protein samples has been developed. This analytical tool will aid in the purification and solubilization of membrane proteins that are ideal for crystallization trials.

Online 20 December 2002


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Acta Cryst. (2003). D59, 84-92  [ doi:10.1107/S0907444902019443 ]

Atomic resolution structure of Erwinia chrysanthemi L-asparaginase

J. Lubkowski, M. Dauter, K. Aghaiypour, A. Wlodawer and Z. Dauter

Synopsis: The crystal structure of E. chrysanthemi L-asparaginase has been refined at 1.0 Å resolution, elucidating the atomic level details of one of the largest asymmetric units studied to date at this level of accuracy.

PDB reference: 1o7j

Online 20 December 2002


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Acta Cryst. (2003). D59, 93-104  [ doi:10.1107/S0907444902019455 ]

The refined atomic structure of carbonic anhydrase II at 1.05 Å resolution: implications of chemical rescue of proton transfer

D. Duda, L. Govindasamy, M. Agbandje-McKenna, C. Tu, D. N. Silverman and R. McKenna

Synopsis: Using synchrotron radiation and a CCD detector, X-ray data have been collected at 100 K for the His64Ala mutant of human carbonic anhydrase II complexed with 4-methylimidazole (4-MI) to a maximal 1.05 Å resolution, allowing full anisotropic least-squares refinement.

PDB reference: 1moo

Online 20 December 2002


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Acta Cryst. (2003). D59, 105-117  [ doi:10.1107/S0907444902020164 ]

Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 Å) at 100 K and atomic resolution (1.11 Å) at 293 K refined anisotropically to small-molecule accuracy

R. Natesh, K. Manikandan, P. Bhanumoorthy, M. A. Viswamitra and S. Ramakumar

Synopsis: The structure of T. aurantiacus xylanase solved to small-molecule accuracy at atomic resolution (1.11 Å) at 293 K and at ultrahigh resolution (0.89 Å) at 100 K provides insights into the plasticity of salt bridges, the temperature-dependent deformation and the water structure of the enzyme, which belongs to the ubiquitous TIM-barrel fold.

PDB references: 1i1x and 1i1w

Online 20 December 2002


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Acta Cryst. (2003). D59, 118-126  [ doi:10.1107/S0907444902020176 ]

A new class of gadolinium complexes employed to obtain high-phasing-power heavy-atom derivatives: results from SAD experiments with hen egg-white lysozyme and urate oxidase from Aspergillus flavus

É Girard, M. Stelter, P. L. Anelli, J. Vicat and R. Kahn

Synopsis: Seven gadolinium complexes are shown to be excellent compounds for the production of heavy-atom derivatives for macromolecular crystallography projects. SAD phasing has been successfully carried out on a series of gadolinium-derivative crystals of two proteins, hen egg-white lysozyme and urate oxidase from A. flavus, leading to high-quality electron-density maps.

Online 20 December 2002


structural genomics papers


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Acta Cryst. (2003). D59, 127-135  [ doi:10.1107/S0907444902018012 ]

Structure of a yeast hypothetical protein selected by a structural genomics approach

S. Eswaramoorthy, S. Gerchman, V. Graziano, H. Kycia, F. W. Studier and S. Swaminathan

Synopsis: The crystal structure of YBL036C has been determined by MIRAS and MAD methods.

PDB references: 1b54 and 1ct5

Online 20 December 2002


crystallization papers


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Acta Cryst. (2003). D59, 136-138  [ doi:10.1107/S0907444902018516 ]

Crystals of trp repressor suitable for high-resolution neutron Laue diffraction studies

B. V. Daniels, D. A. A. Myles, V. T. Forsyth and C. L. Lawson

Synopsis: Preliminary neutron-diffraction measurements of E. coli trp repressor crystals demonstrate that it will be possible to obtain a full-atom neutron structural model of a DNA-binding protein plus its associated solvent.

Online 20 December 2002


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Acta Cryst. (2003). D59, 139-141  [ doi:10.1107/S0907444902018280 ]

Crystallization and preliminary X-ray analysis of Alicyclobacillus acidocaldarius endoglucanase CelA

K. Eckert, H. A. Ernst, E. Schneider, S. Larsen and L. Lo Leggio

Synopsis: Crystallization of family 9 A. acidocaldarius CelA is reported. The crystals are unusual in that they do not bind the dye IZIT in the mother liquor and do not dissolve in the protein-storage buffer or water for several weeks. Collection of a data set to 3.0 Å resolution and initial molecular-replacement searches are reported.

Online 20 December 2002


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Acta Cryst. (2003). D59, 142-145  [ doi:10.1107/S0907444902019066 ]

Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme

V. Grum-Tokars, M. Milovanovic and J. E. Wedekind

Synopsis: An all-RNA 64-mer hairpin ribozyme has been crystallized in a form suitable for X-ray diffraction analysis at 3.35 Å resolution. The construct contains the U39C substitution, which enhances catalytic efficiency and represents the minimal catalytic motif formed by intermolecular docking of two helix-loop-helix domains. The crystallization strategy and results are presented.

Online 20 December 2002


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Acta Cryst. (2003). D59, 146-149  [ doi:10.1107/S0907444902018024 ]

Crystallization and preliminary crystallographic analysis of a partial extracellular fragment of a sperm membrane protein YWK-II/APPH related to the Alzheimer [beta]A4-amyloid precursor protein

M. Yang, B. Liu, X. Zhang, W. Zhou, F. Gao, H. Pang, S. Miao, L. Wang and Z. Rao

Synopsis: A partial extracellular fragment of a sperm membrane protein YWK-II protein/APPH related to the Alzheimer [beta]A4-amyloid precursor protein has been recloned, expressed in E. coli, crystallized and a complete native data set has been collected at 2.8 Å resolution.

Online 20 December 2002


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Acta Cryst. (2003). D59, 150-151  [ doi:10.1107/S0907444902017547 ]

Expression, crystallization and preliminary X-ray analysis of isomaltulose synthase (PalI) from Klebsiella sp. LX3

N. Li, D. Zhang, L.-H. Zhang and K. Swaminathan

Synopsis: The first crystallographic study, at 2.2 Å resolution, of an enzyme that is involved with both hydrolysis and isomerization of sucrose.

Online 20 December 2002


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Acta Cryst. (2003). D59, 152-154  [ doi:10.1107/S0907444902018292 ]

Preliminary X-ray crystallographic analysis of tRNA pseudouridine 55 synthase from the thermophilic eubacterium Thermotoga maritima

J. Wouters, C. Tricot, V. Durbecq, M. Roovers, V. Stalon and L. Droogmans

Synopsis: Overexpression, purification and crystallization of T. maritima TruB allowed collection of a complete data set to 2.0 Å resolution.

Online 20 December 2002


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Acta Cryst. (2003). D59, 155-157  [ doi:10.1107/S0907444902018358 ]

Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis

E. V. Blagova, V. M. Levdikov, K. Tachikawa, A. L. Sonenshein and A. J. Wilkinson

Synopsis: The GTP-responsive transcriptional repressor CodY from B. subtilis has been crystallized in a number of forms in the presence and absence of ligands. A complete data set to 3.5 Å spacing has been collected.

Online 20 December 2002


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Acta Cryst. (2003). D59, 158-160  [ doi:10.1107/S090744490201836X ]

X-ray analysis of two antibiotic-synthesizing bacterial ester hydrolases: preliminary results

T. R. M. Barends, C. M. H. Hensgens, J. J. Polderman-Tijmes, P. A. Jekel, E. de Vries, D. B. Janssen and B. W. Dijkstra

Synopsis: Good-quality crystals have been obtained of two microbial [alpha]-amino-acid ester hydrolases, enzymes of potential use in antibiotic production. One enzyme crystallizes in two space groups, one of which has extremely large unit-cell parameters.

Online 20 December 2002


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Acta Cryst. (2003). D59, 161-162  [ doi:10.1107/S0907444902018504 ]

Jel44 monoclonal Fab fragment specific for HPr of the phosphoenolpyruvate:sugar phosphotransferase system of Escherichia coli and the complex of Jel44 Fab fragment with HPr: preparation, crystallization and preliminary crystallographic analysis

J. Gulyaeva-Tcherkassova, S. L. Labiuk, J. S. Lee, E. B. Waygood and L. T. J. Delbaere

Synopsis: A Jel44 monoclonal Fab fragment specific for E. coli HPr has been purified. Crystals of the Jel44 Fab fragment diffracted to a resolution of 4.6 Å, while crystals of the novel complex of the Jel44 Fab fragment with HPr diffracted to a resolution of 2.5 Å.

Online 20 December 2002


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Acta Cryst. (2003). D59, 163-165  [ doi:10.1107/S0907444902018863 ]

Crystallization and preliminary X-ray studies of thymus and activation-regulated chemokine (TARC)

O. A. Asojo, S. Cater, D. M. Hoover, C. Boulègue, W. Lu and J. Lubkowski

Synopsis: Preliminary crystallographic studies of synthetically prepared thymus and activation-regulated chemokine (TARC) in the triclinic, hexagonal and tetragonal systems are described.

Online 20 December 2002


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Acta Cryst. (2003). D59, 166-167  [ doi:10.1107/S0907444902018905 ]

Crystallization and preliminary X-ray crystallographic analysis of malonyl-CoA decarboxylase from Rhizobium leguminosarum bv. trifolii

J.-S. Jung, D.-J. Baek, G.-Y. Lee, Y.-S. Kim and B.-H. Oh

Synopsis: Malonyl-CoA decarboxylase of a Rhizobium species was crystallized. This enzyme shares 30% sequence identity with human homology.

Online 20 December 2002


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Acta Cryst. (2003). D59, 168-170  [ doi:10.1107/S0907444902019248 ]

SseA, a 3-mercaptopyruvate sulfurtransferase from Escherichia coli: crystallization and preliminary crystallographic data

A. Spallarossa, A. Carpen, F. Forlani, S. Pagani, M. Bolognesi and D. Bordo

Synopsis: The in vivo role and substrate specificity of sulfurtransferase enzymes has been greatly debated. SseA, a 3-mercaptopyruvate:cyanide sulfurtransferase from E. coli, has been crystallized in a tetragonal crystal form suitable for X-ray crystallographic investigations.

Online 20 December 2002


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Acta Cryst. (2003). D59, 171-173  [ doi:10.1107/S0907444902019546 ]

Crystallization and preliminary X-ray diffraction studies of Hje, a Holliday junction resolving enzyme from Sulfolobus solfataricus

C. L. Middleton, J. L. Parker, D. J. Richard, M. F. White and C. S. Bond

Synopsis: The Holliday junction resolving enzyme Hje from S. solfataricus has been crystallized. Preliminary crystallographic analysis indicates a possible difference in dimeric arrangement to the homologous enzyme Hjc.

Online 20 December 2002


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Acta Cryst. (2003). D59, 174-176  [ doi:10.1107/S0907444902019649 ]

Crystallization and preliminary X-ray diffraction studies of a novel alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix

J. E. Guy, M. N. Isupov and J. A. Littlechild

Synopsis: Crystals of a zinc-containing alcohol dehydrogenase from the hyperthermophilic archaeon A. pernix have been grown by the sitting-drop vapour-diffusion technique from recombinant protein expressed in E. coli and show diffraction to 1.5 Å resolution. The anomalous diffraction from zinc at two wavelengths and twofold NCS averaging have resulted in an interpretable electron-density map.

Online 20 December 2002


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Acta Cryst. (2003). D59, 177-179  [ doi:10.1107/S0907444902019686 ]

Crystallographic characterization of the radixin FERM domain bound to the C-terminal region of the human Na+/H+-exchanger regulatory factor (NHERF)

S. Terawaki, R. Maesaki, K. Okada and T. Hakoshima

Synopsis: Crystals of complexes between the radixin FERM domain and the C-terminal regions of NHERF and NHERF2 have been obtained.

Online 20 December 2002


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Acta Cryst. (2003). D59, 180-182  [ doi:10.1107/S0907444902019698 ]

Crystallization and preliminary X-ray crystallographic studies of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae

M.-J. Ku, H.-J. Yoon, H. J. Ahn, H.-W. Kim, S.-H. Baek and S. W. Suh

Synopsis: CMP-KDO synthetase from H. influenzae was crystallized. X-ray diffraction data were collected to 2.2 Å from an SeMet crystal.

Online 20 December 2002


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Acta Cryst. (2003). D59, 183-184  [ doi:10.1107/S0907444902019716 ]

Crystallization and preliminary X-ray crystallographic analysis of tRNA(m1G37)methyltransferase from Haemophilus influenzae

H.-W. Kim, H. J. Ahn, H.-J. Yoon, H. W. Kim, S.-H. Baek and S. W. Suh

Synopsis: tRNA(m1G37)methyltransferase (TrmD) from H. influenzae was crystallized. X-ray data have been collected to 1.85 Å.

Online 20 December 2002


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Acta Cryst. (2003). D59, 185-187  [ doi:10.1107/S0907444902019777 ]

Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex

D. Temiakov, T. H. Tahirov, M. Anikin, W. T. McAllister, D. G. Vassylyev and S. Yokoyama

Synopsis: A phage T7 RNA polymerase elongation complex containing 8 bp of RNA-DNA hybrid and 10 bp of downstream DNA with a total molecular mass of ~110 kDa was crystallized. A complete diffraction data set was collected at 2.6 Å resolution. The structure determination and refinement are in progress.

Online 20 December 2002


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Acta Cryst. (2003). D59, 188-190  [ doi:10.1107/S0907444902020395 ]

Preliminary crystallographic analysis of 3-chlorocatechol 1,2-dioxygenase of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol

M. Ferraroni, M. Y. Ruiz Tarifa, A. Scozzafava, I. P. Solyanikova, M. P. Kolomytseva, L. Golovleva and F. Briganti

Synopsis: 3-Chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium R. opacus (erythropolis) 1CP, an enzyme involved in the specific cleavage of 3-chlorocatechol, which is an intermediate in the aerobic biodegradation of 2-chlorophenol, has been crystallized.

Online 20 December 2002


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Acta Cryst. (2003). D59, 191-193  [ doi:10.1107/S0907444902020723 ]

Crystallization and preliminary crystallographic analysis of the kinase-recruitment domain of the PP2C-type phosphatase RsbU

S. Dutta and R. J. Lewis

Synopsis: The kinase-recruitment domain of the PP2C-type phosphatase RsbU from B. subtilis has been crystallized in a form that diffracts to 1.6 Å resolution using synchrotron radiation.

Online 20 December 2002


short communications


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Acta Cryst. (2003). D59, 194-196  [ doi:10.1107/S0907444902019741 ]

Application of a two-liquid system to sitting-drop vapour-diffusion protein crystallization

H. Adachi, K. Takano, M. Morikawa, S. Kanaya, M. Yoshimura, Y. Mori and T. Sasaki

Synopsis: A new method of protein crystallization, the floating-drop vapour-diffusion technique, has been developed.

Online 20 December 2002


international union of crystallography


 

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Acta Cryst. (2003). D59, 197-202  [ doi:10.1107/S0907444902023144 ]

Notes for authors 2003

Online 20 December 2002


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