Post-crystallization treatments for improving diffraction quality of protein crystals

This review provides a compilation of post-crystallization methods that can convert poorly diffracting crystals into data-quality crystals. Protocols for annealing, dehydration, soaking and cross-linking are outlined and examples of some spectacular changes in crystal quality are provided.

Regular arrangement of periodates bound to lysozyme

The structure of the periodate complex of lysozyme has been determined, refined and analyzed.

Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper

The crystal structures of oxidised and reduced nitrite reductase from R. sphaeroides give new insight into the pH dependence of nitrite binding to the active site.

Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms

The crystal structures of naphthoate synthase (MenB) and its complex with the product naphthoyl-CoA have been determined by X-ray crystallography at resolutions of 2.15 and 2.30 Å, respectively. The native structure shows several flexible regions around the active site which are only partly rigidified by the bound ligand.

Structure of a putative 2′-5′ RNA ligase from Pyrococcus horikoshii

The crystal structure of a putative 2′-5′ RNA ligase from P. horikoshii was solved and compared with a Thermus thermophilus homologue and the structurally related cyclic phosphodiesterase.

Structure of glyceraldehyde-3-phosphate de­hydrogenase from Plasmodium falciparum

The structure of P. falciparum GAPDH has been solved to 2.6 Å resolution with one molecule of NAD⁺ bound per subunit. Amino-acid substitutions which cluster in a groove about the R dyad suggest a potential binding site for haem, which is known to specifically inhibit the Plasmodium enzyme.

Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid

The X-ray structure of the enzyme 5-aminolaevulinic acid dehydratase (ALAD) from yeast complexed with the competitive inhibitor 5-hydroxylaevulinic acid has been determined at a resolution of 1.9 Å.

Improving radiation-damage substructures for RIP

A simple method for treating RIP data is presented which improves the quality of RIP substructures as well as the phases from downstream phasing applications.

Overcoming the false-minima problem in direct methods: structure determination of the packaging enzyme P4 from bacteriophage φ13

The problems encountered during the phasing and structure determination of the packaging enzyme P4 from bacteriophage φ13 which arise from the arrangement of the four hexamers comprising the crystallographic asymmetric unit are described.

Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine

The malarial purine nucleoside phosphorylase (PNP) in complexes with inosine and with sulfate, are reported. These structures are compared with a previous structure of P. falciparum PNP in complex with a transition-state inhibitor.

Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold

The cystine-knot protein EETI-II is shown to be particularly rigid.

On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength

Based on the evaluation of a large number of experiments carried out at different X-ray wavelengths with respect to the anomalous signal-to-noise ratio, the optimum wavelength for diffraction data collection was found to be close to 2.1 Å irrespective of the nature of the anomalously scattering substructure.

Structures of aminoglycoside acetyltransferase AAC(6′)-Ii in a novel crystal form: structural and normal-mode analyses

The structure of the antibiotic resistance factor AAC(6′)-Ii in complex with coenzyme A has been determined in a new crystal form. Comparison of this structure with the previously determined complex and in combination with normal-mode analysis reveals conformational plasticity that may be important to enzymatic mechanism.

Protein crystallization in hydrogel beads

The use of hydrogel beads for the crystallization of proteins is explored in this contribution.

Radiation-induced site-specific damage of mercury derivatives: phasing and implications

Analysis of data collected from Hg-derivatized crystals reveals that mercury–cysteine bonds are very susceptible to radiation damage.

Bulk-solvent correction in large macromolecular structures

It is shown that the standard bulk-solvent corrrection, as implemented in CNS, can lead to incorrect results in the case of large macromolecular structures. A modified method of the solvent mask definition is proposed.

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions

Heavy-atom Database System is a program that assists heavy-atom derivatization of proteins. On the basis of amino-acid sequence/motif and crystallization conditions, the program suggests potential heavy-atom reagents for any target protein by searching against a database of known heavy-atom derivatives.

Surface-entropy reduction used in the crystallization of human choline acetyltransferase

Surface-entropy reduction was used to obtain high-quality crystals of human choline acetyltransferase.

Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Corrigendum

A corrigendum to the paper by Liu et al. (2005), Acta Cryst. D61, 520–527.

Unravelling the structural chemistry of the colouration mechanism in lobster shell. Erratum

An erratum to the paper by Chayen et al. (2003), Acta Cryst. D59, 2072–2082.