Biological Crystallography

 

Acta Cryst. (2009). D65, 623-624  [ doi:10.1107/S0907444909020861 ]

The Max-Inf2/Lorentz Center workshop on New algorithms in macromolecular crystallography and electron microscopy

N. S. Pannu, R. B. G. Ravelli and J. P. Abrahams

Synopsis: A summary of the 2008 New algorithms in macromolecular crystallography and electron microscopy Max-Inf2/Lorentz Center workshop in Leiden is given.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 625-632  [ doi:10.1107/S0907444909003163 ]

Unit-cell determination from randomly oriented electron-diffraction patterns

L. Jiang, D. Georgieva, H. W. Zandbergen and J. P. Abrahams

Synopsis: An algorithm is described that calculates the most likely primitive unit cell given a set of randomly oriented electron-diffraction patterns with unknown angular relationships.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 633-643  [ doi:10.1107/S0907444909010695 ]

Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit

F. Ni, B. K. Poon, Q. Wang and J. Ma

Synopsis: The application of a new normal-mode-based X-ray crystallographic refinement method to a total of eight structures of moderate resolution is illustrated.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 644-650  [ doi:10.1107/S090744490900969X ]

Cluster analysis for phasing with molecular replacement: a feasibility study

A. Buehler, L. Urzhumtseva, V. Y. Lunin and A. Urzhumtsev

Synopsis: Molecular replacement with the simultaneous use of several search functions may solve the phase problem when the conventional molecular-replacement procedure fails to identify the solution.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 651-658  [ doi:10.1107/S0907444909008671 ]

UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

X. Siebert and J. Navaza

Synopsis: UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 659-671  [ doi:10.1107/S0907444909011433 ]

Parallel, distributed and GPU computing technologies in single-particle electron microscopy

M. Schmeisser, B. C. Heisen, M. Luettich, B. Busche, F. Hauer, T. Koske, K.-H. Knauber and H. Stark

Synopsis: An introduction to the current paradigm shift towards concurrency in software.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 672-678  [ doi:10.1107/S0907444909012049 ]

Introducing robustness to maximum-likelihood refinement of electron-microsopy data

S. H. W. Scheres and J.-M. Carazo

Synopsis: An expectation-maximization algorithm for maximum-likelihood refinement of electron-microscopy data is presented that is based on finite mixtures of multivariate t-distributions. Compared with the conventionally employed Gaussian mixture model, the t-distribution provides robustness against outliers in the data.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 679-689  [ doi:10.1107/S0907444909012876 ]

Confidence intervals for fitting of atomic models into low-resolution densities

N. Volkmann

Synopsis: This paper describes procedures for obtaining confidence intervals for coordinate locations resulting from the fitting of atomic models into low-resolution densities.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 690-696  [ doi:10.1107/S090744490901991X ]

Interpretation of very low resolution X-ray electron-density maps using core objects

P. Heuser, G. G. Langer and V. S. Lamzin

Synopsis: The interpretation of a 20 Å resolution electron-density map using segmentation and pattern-recognition-based identification of domain shapes is described.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 697-703  [ doi:10.1107/S0907444909012086 ]

What can we learn by computing ¹³C chemical shifts for X-ray protein models?

Y. A. Arnautova, J. A. Vila, O. A. Martin and H. A. Scheraga

Synopsis: The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed ¹³C chemical shifts in solution.

Online 20 June 2009

 

Acta Cryst. (2009). D65, 704-716  [ doi:10.1107/S090744490901230X ]

Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexate

O. Senkovich, N. Schormann and D. Chattopadhyay

Synopsis: In order to gain a detailed understanding of the structure-function relationship of T. cruzi dihydrofolate reductase (DHFR), the three-dimensional structure of this protein in complex with various ligands is being studied. Here, the crystal structures of T. cruzi DHFR-TS with three different compositions of the DHFR domain are reported: the folate-free state, the complex with the lipophilic antifolate trimetrexate and the complex with the classical antifolate methotrexate.

PDB references: 2h2q, 3clb and 3cl9

Online 20 June 2009

 

Acta Cryst. (2009). D65, 717-723  [ doi:10.1107/S0907444909012165 ]

A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta)

E. Toyota, D. Iyaguchi, H. Sekizaki, M. Tateyama and K. K. S. Ng

Synopsis: The crystal structures of three isoforms of anionic trypsin from chum salmon reveal a structural basis for their differences in catalytic efficiency and explain how small differences in sequence and structure allow enzymes to perform their biological functions in a wide range of environments.

PDB references: 2zpq, 2zpr and 2zps

Online 20 June 2009

 

Acta Cryst. (2009). D65, 724-732  [ doi:10.1107/S0907444909013328 ]

Structures of mannose-6-phosphate isomerase from Salmonella typhimurium bound to metal atoms and substrate: implications for catalytic mechanism

S. R. Sagurthi, G. Gowda, H. S. Savithri and M. R. N. Murthy

Synopsis: The X-ray crystal structures of mannose-6-phosphate isomerase from S. typhimurium in the apo form (with no metal bound), the holo form (with zinc), bound to yttrium (at an inhibitory site) and complexed with the cyclic form of the substrate fructose 6-phosphate and Zn²⁺ are reported.

PDB references: 2wfp, 3hlm, 3hlw and 3hly

Online 20 June 2009