Biological Crystallography

 

Acta Cryst. (2006). D62, 227-238  [ doi:10.1107/S0907444905040680 ]

Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry

F. Fabiola, A. Korostelev and M. S. Chapman

Synopsis: Elimination of the strongest correlations between test-set and working-set reflections reduces R^free bias to acceptable levels when non-crystallographic symmetry is low-order. Bias can not be completely eliminated in the presence of high-order non-crystallographic symmetry, but bias reduction allows optimization of the weights for stereochemically restrained refinement.

Online 22 February 2006

 

Acta Cryst. (2006). D62, 239-245  [ doi:10.1107/S0907444905041077 ]

Evaluation of crystalline objects in crystallizing protein droplets based on line-segment information in greyscale images

K. Kawabata, M. Takahashi, K. Saitoh, H. Asama, T. Mishima, M. Sugahara and M. Miyano

Synopsis: The method presented here evaluates crystalline objects in crystallization droplets.

Online 22 February 2006

 

Acta Cryst. (2006). D62, 246-252  [ doi:10.1107/S0907444905041260 ]

Structure of the aspartic protease plasmepsin 4 from the malarial parasite Plasmodium malariae bound to an allophenylnorstatine-based inhibitor

J. C. Clemente, L. Govindasamy, A. Madabushi, S. Z. Fisher, R. E. Moose, C. A. Yowell, K. Hidaka, T. Kimura, Y. Hayashi, Y. Kiso, M. Agbandje-McKenna, J. B. Dame, B. M. Dunn and R. McKenna

Synopsis: The crystal structure of P. malariae plasmepsin 4 (PmPM4) complexed with the allophenylnorstatine-based inhibitor, KNI-764, is reported. The inhibitor is shown to be bound to PmPM4 in an unexpected orientation with allophenylnorstatine occupying the S1' pocket.

PDB reference: 2anl

Online 22 February 2006

 

Acta Cryst. (2006). D62, 253-261  [ doi:10.1107/S0907444905041429 ]

UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops

X. Vernede, B. Lavault, J. Ohana, D. Nurizzo, J. Joly, L. Jacquamet, F. Felisaz, F. Cipriani and D. Bourgeois

Synopsis: The combined use of non-fluorescent sample holders and short UV-laser pulses to excite the fluorescence of aromatic residues is an efficient tool to visualize protein crystals mounted on synchrotron beamlines. Putative structural damage induced by the short UV-laser pulses was not observed.

PDB references: 2c8q, 2c8r, 2c8o and 2c8p

Online 22 February 2006

 

Acta Cryst. (2006). D62, 262-270  [ doi:10.1107/S0907444905041363 ]

Structure of the novel -amylase AmyC from Thermotoga maritima

A. Dickmanns, M. Ballschmiter, W. Liebl and R. Ficner

Synopsis: The crystal structure of a previously unidentified amylase (AmyC) from the hyperthermophilic organism Thermotoga maritima has been determined at 2.2 Å resolution by means of MAD.

PDB reference: 2b5d

Online 22 February 2006

 

Acta Cryst. (2006). D62, 271-279  [ doi:10.1107/S0907444905041648 ]

Automated classification of protein crystallization images using support vector machines with scale-invariant texture and Gabor features

S. Pan, G. Shavit, M. Penas-Centeno, D.-H. Xu, L. Shapiro, R. Ladner, E. Riskin, W. Hol and D. Meldrum

Synopsis: A new classification system is developed to automatically identify crystal growth in images with a very low false-negative and a moderate false-positive rate. It uses a support vector machine trained on texture and wavelet features and includes a new algorithm to find the drop area within the image.

Online 22 February 2006

 

Acta Cryst. (2006). D62, 280-289  [ doi:10.1107/S0907444905041909 ]

New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)

H. Miyatake, T. Hasegawa and A. Yamano

Synopsis: Iodination by VIL and HYPER-VIL.

PDB references: 2d8o, 2d8p, 2d8w, 2d91, 2dan and 2d98

Online 22 February 2006

 

Acta Cryst. (2006). D62, 290-301  [ doi:10.1107/S0907444905042289 ]

High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase

J. L. Jenkins and J. J. Tanner

Synopsis: The first high-resolution crystal structure of human D-glyceraldehyde-3-phosphate dehydrogenase is reported. The structure is used to predict possible binding sites for an anti-apoptosis compound and the E3 ubiquitin ligase Siah1.

PDB reference: 1u8f

Online 22 February 2006

 

Acta Cryst. (2006). D62, 302-311  [ doi:10.1107/S0907444905042654 ]

Efficient characterization of protein secondary structure in terms of screw motions

G. R. Kneller and P. Calligari

Synopsis: A simple and efficient method is presented to describe the secondary structure of proteins in terms of orientational distances between consecutive peptide planes and local helix parameters.

Online 22 February 2006

 

Acta Cryst. (2006). D62, 312-323  [ doi:10.1107/S0907444905042642 ]

Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor

D. E. Hurt, J. Widom and J. Clardy

Synopsis: The structure of P. falciparum dihydroorotate dehydrogenase (DHODH) bound to the human DHODH inhibitor A77 1726 explains the poor binding affinity of the inhibitor and provides critical insight for the design of potential antimalarials.

PDB reference: 1tv5

Online 22 February 2006

 

Acta Cryst. (2006). D62, 324-330  [ doi:10.1107/S0907444905043179 ]

Structure of the carboxy-terminal PH domain of pleckstrin at 2.1 Å

S. G. Jackson, Y. Zhang, X. Bao, K. Zhang, R. Summerfield, R. J. Haslam and M. S. Junop

Synopsis: The crystal structure of the carboxy-terminal PH domain of pleckstrin is reported at 2.1 Å and comparisons are made between this structure and the recently reported solution structure of the same domain as well as other relevant PH domains.

PDB reference: 1zm0

Online 22 February 2006

 

Acta Cryst. (2006). D62, 331-338  [ doi:10.1107/S0907444905043210 ]

Structure of an RNA duplex r(GGCG_BrUGCGCU)₂ with terminal and internal tandem G·U base pairs

R. Utsunomiya, K. Suto, D. Balasundaresan, A. Fukamizu, P. K. R. Kumar and H. Mizuno

Synopsis: The structure of the RNA duplex reveals detailed insights of terminal and internal tandem G·U base pairs about the geometry including the stacking interactions.

PDB reference: 2ao5

Online 22 February 2006

 

Acta Cryst. (2006). D62, 339-346  [ doi:10.1107/S0907444906000813 ]

Trace fluorescent labeling for high-throughput crystallography

E. Forsythe, A. Achari and M. L. Pusey

Synopsis: Covalent trace (<1%) labeling of proteins with a visible fluorescent probe facilitates finding crystals during the screening process.

Online 22 February 2006

 

Acta Cryst. (2006). D62, 347-348  [ doi:10.1107/S0907444906002010 ]

Structure Determination by X-ray Crystallography

Online 22 February 2006