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

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

Unit-cell determination from randomly oriented electron-diffraction patterns

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.

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

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

Cluster analysis for phasing with molecular replacement: a feasibility study

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.

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

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.

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

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

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

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.

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

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

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

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

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

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^α chemical shifts in solution.

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

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.

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

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.

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

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.