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Acta Cryst. (2014). A70, C338
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The use of prior chemical knowledge such as bond lengths, bond angles about constituent blocks of macromolecules and ligands is an essential part of macromolecular crystal structure analysis. One of the reliable sources of such chemical knowledge is small molecule database where small molecule crystal structures have been analysed against high-resolution, high-quality experimental data. Furthermore, vast amount of data in small molecule database provide comprehensive coverage of flexible chemical environment and enable proper statistical analysis to avoid biased representation of those chemical properties. This presentation describes our work on organization of the data from open-access and daily-updated small molecule database, Crystallography Open Database(COD) [1], into a new generation of CCP4 monomer library (Dictionary), a container of prior chemical knowledge [2]. In order to describe specific environment atoms are in, they are classified into different atomic types based on local graphs and some basic chemical properties of atoms. This scheme can be applied to any small molecule databases. The atom types, and values of bond lengths and bond associated with them, are further clustered into a hierarchical tree and an isomorphism-mapping algorithm is implemented to facilitate fast search among a large number of atom types (typically several millions). This also provides a mechanism to derive reliable values for bond lengths and angles of novel ligands. Metal and non-organic atoms are treated differently with organic ones. The original data in COD are curated using several criteria and further statistical analysis on derived values of bond lengths and angles are allow to extract reliable chemical information from such databanks as COD. There are several software tools associated with new dictionary including 1) generate "ideal" bond lengths and angles for unknown ligand; 2) generate starting coordinates to represent one of the conformation of the ligand under consideration.

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Acta Cryst. (2014). A70, C348
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Membrane proteins and large assemblies are currently a major focus of molecular biology and molecular medicine. Due to their size and flexibility, these structures may only yield poor quality crystals for which diffraction intensities can be measured to merely mid-low resolution. Nevertheless, these data contain valuable structural information. Here, it will be shown how new features in COOT [1], REFMAC5 [2] and ProSMART [3] can help to exploit low resolution data for model building and refinement, as well as aid model validation. Refinement at low resolution can be stabilised with regularisers, such as jelly-body and external restraints. These allow to routinely obtain good quality models even in cases where only low-resolution data are available (e.g. >3Å). External restraints (available for protein and DNA/RNA) exploit structural prior knowledge, utilising the assertion that local interatomic distances should agree with previous observations. Sources for such prior knowledge include isomorphous and homologous structures, hydrogen bonding patterns, and typical conformations of secondary structure elements. Importantly, global rigidity is not enforced by these restraints - the approach presented allows for dramatic conformational differences between target and reference models. Consequently, restraints may be generated using homologous reference models resolved in different crystal forms. COOT facilitates model building at low resolution by removing degrees of freedom through so-called "backrub rotamers" and torsion angle restraints, as well as providing semi-automatic building options such as model morphing and jiggle fit . Map sharpening and blurring, now available in both COOT and REFMAC5, can be employed to provide further insight regarding the validity of a model, as well as aiding the model building process. General guidelines for the application of these features are provided, along with examples demonstrating their usage.

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Acta Cryst. (2014). A70, C494
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Structural comparison often aids insight into the function and mechanics of biological macromolecules. To make such analyses more accessible, we present the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART), which is designed to allow fast but detailed comparative analysis of macromolecular structures despite potential dissimilarities in global arrangement, such as domain motion and distortion. Whilst obtaining a residue alignment between structures is a prerequisite for comparative analysis, conventional alignment methods may fail in cases where conformational differences are dramatic. However, ProSMART achieves a conformation-independent structural alignment by focusing purely on local dissimilarities, rather than enforcing chain/domain rigidity. This allows the sensible comparison of protein (or DNA/RNA) structures in the presence of conformational change. ProSMART allows analysis of the structural conservation of local backbone and side chains in a wide variety of scenarios - the method is sensitive enough to allow identification of subtle dissimilarities between structures sharing high sequence homology, whilst being versatile enough to allow identification of local similarities between more distantly-related structures. In addition, ProSMART can be used for the identification of conserved rigid substructures, which may or may not represent functional domains. ProSMART is also used for the generation of external restraints for use in crystallographic refinement. Results from ProSMART can be visualised in either CCP4mg or PyMOL. All residue-based scores are illustrated using intuitive colour gradients, allowing easy visual assessment of local backbone and side chain conservation. Complementary structural comparison tools such as ProSMART can help break the complexity of the constantly growing pool of available structural data into a more readily accessible form, and consequently may aid biological insight into macromolecular structures.

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Acta Cryst. (2014). A70, C777
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We have developed methods for processing area detector data collected from samples containing several crystal lattices, and implemented these into the data processing program Mosflm and its GUI iMosflm [1]. In particular we have extended the following processes: (1) modified autoindexing routines recognize different lattices and display this information in iMosflm in a clear and concise way, allowing the user to choose how to proceed. (2) multiple lattice information is used to determine which data are used in refinement of crystal parameters and which (e.g. overlapped reflections) should be excluded. (3) observations are integrated in each lattice and flagged in the output reflection file (written in the MTZ format) to indicate whether they arise from a single lattice or from overlapped reflections from multiple lattices. The choice of lattice in the latter two stages of data processing is made simple in iMosflm. The information regarding reflection overlap can now be processed correctly in the merging and scaling steps by the programs Feckless, Pointless and Aimless [2]. The refinement program RefMac [3] has been modified to make use of the extra information from multiple lattices. We will discuss these improvements to processing and present early results from their implementation.

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Acta Cryst. (2014). A70, C1051
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Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle electron cryo-microscopy. The resolution of 3.2 Ångstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site and a putative membrane docking site.
Keywords: Ribosome; Cryo-EM.
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