Sven Hovmöller

CRISP: crystallographic image processing on a personal computer

Abstract A computer program system, CRISP, for crystallographic image processing (CIP), has been developed. CRISP runs on a standard personal computer (PC), and is considerably faster than previous systems for CIP. High-resolution electron microscopy (HREM) images are digitized by a CCD camera and directly transferred to the PC via a frame grabber. CRISP has been designed with strong emphasis on user friendliness. Thus, installation takes only a few minutes, a full processing of an HREM image takes less than 20 minutes, all operations are carried out with a mouse, and all the crystallography needed for 2D analysis of images is programmed into CRISP.

Conformations of amino acids in proteins

The main-chain conformations of 237 384 amino acids in 1042 protein subunits from the PDB were analyzed with Ramachandran plots. The populated areas of the empirical Ramachandran plot differed markedly from the classical plot in all regions. All amino acids in alpha-helices are found within a very narrow range of phi, psi angles. As many as 40% of all amino acids are found in this most populated region, covering only 2% of the Ramachandran plot. The beta-sheet region is clearly subdivided into two distinct regions. These do not arise from the parallel and antiparallel beta-strands, which have quite similar conformations. One beta region is mainly from amino acids in random coil. The third and smallest populated area of the Ramachandran plot, often denoted left-handed alpha-helix, has a different position than that originally suggested by Ramachandran. Each of the 20 amino acids has its own very characteristic Ramachandran plot. Most of the glycines have conformations that were considered to be less favoured. These results may be useful for checking secondary-structure assignments in the PDB and for predicting protein folding.

Structure of the polycrystalline zeolite catalyst IM-5 solved by enhanced charge flipping

Despite substantial advances in crystal structure determination methodology for polycrystalline materials, some problems have remained intractable. A case in point is the zeolite catalyst IM-5, whose structure has eluded determination for almost 10 years. Here we present a charge-flipping structure-solution algorithm, extended to facilitate the combined use of powder diffraction and electron microscopy data. With this algorithm, we have elucidated the complex structure of IM-5, with 24 topologically distinct silicon atoms and an unusual two-dimensional medium-pore channel system. This powerful approach to structure solution can be applied without modification to any type of polycrystalline material (e.g., catalysts, ceramics, pharmaceuticals, complex metal alloys) and is therefore pertinent to a diverse range of scientific disciplines.

Collecting 3D electron diffraction data by the rotation method

Abstract A new method for collecting complete three-dimensional electron diffraction data is described. Diffraction data is collected by combining electron beam tilt at many very small steps, with rotation of the crystal in a few but large steps. A number of practical considerations are discussed, as well as advantages and disadvantages compared to other methods of collecting electron diffraction data.

Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing

Implementation of the RED software package for automated collection and processing of rotation electron diffraction data is described.

ELD — a computer program system for extracting intensities from electron diffraction patterns

Abstract A computer program system, ELD, for extracting intensities from electron diffraction (ED) patterns has been developed. ELD runs on a personal computer (PC). Electron diffraction patterns are digitized using a CCD camera, and the data is transferred to the PC via a frame grabber. The lattice vectors and the shape and size of the diffraction spots are first determined, and based upon this information the strategy for extracting the electron diffraction intensities is decided by ELD. It is possible to merge several diffraction patterns taken with different exposure times, whereby both very strong and very weak reflections can be measured. Quantified electron diffraction data can be useful both for chemical applications, such as refining crystal structures, previously solved by crystallographic image processing (CIP), in materials science and for physical applications.

THE STRUCTURE OF CRYSTALLINE BACTERIAL SURFACE LAYERS

THREE-DIMENSIONAL STRUCTURES OF S-LAYERS 1. Classification of S-layers According to Symmetry 2. Hexagonal S-layers (a) Sulfolobus acidocaldarius (b) Thermoproteus tenax (c) Synechocystis sp. CLII (d) Eubacterium sp. AHN 990 (e) Clostridium thermohydrosulfuricum (f) Deinococcus radiodurans (g) Aquaspirillum serpens (h) Acetooenium kivui (i) Bacteroides buccae 3. Tetragonal S-layers (a) Bacillus sphae~icus (b) Sporosarcina ureae (c) Clostridium aceticum (d) Clostridium thermosaccharolyticum (e) Eubacterium sp. ES4C (f) Aeromonas hydrofila (g) Azotobacter vinelandi (h) Desulfurococcus mobilis Oblique S-layers (a) Methanospirillum hungatei 4.

Prediction of zinc-binding sites in proteins from sequence

MOTIVATION Motivated by the abundance, importance and unique functionality of zinc, both biologically and physiologically, we have developed an improved method for the prediction of zinc-binding sites in proteins from their amino acid sequences. RESULTS By combining support vector machine (SVM) and homology-based predictions, our method predicts zinc-binding Cys, His, Asp and Glu with 75% precision (86% for Cys and His only) at 50% recall according to a 5-fold cross-validation on a non-redundant set of protein chains from the Protein Data Bank (PDB) (2727 chains, 235 of which bind zinc). Consequently, our method predicts zinc-binding Cys and His with 10% higher precision at different recall levels compared to a recently published method when tested on the same dataset. AVAILABILITY The program is available for download at www.fos.su.se/~nanjiang/zincpred/download/

Structure of Ti2P solved by three-dimensional electron diffraction data collected with the precession technique and high-resolution electron microscopy

The crystal structure of Ti(2)P has been analysed using electron diffraction and high-resolution electron-microscopy techniques. A new unit cell was found, the compound is hexagonal with a = 19.969 (1) and c = 3.4589 (1) A. The structure was first solved in space group P-62m in projection using direct methods on electron diffraction data from the [001] zone axis. A three-dimensional solution was obtained using again direct methods but on a three-dimensional set of electron diffraction data recorded with the precession technique. Ti(2)P is a distorted Fe(2)P structure and, based on high-resolution images, it is possible to explain that the tripling of the unit cell is due to the ordering of P vacancies that reduces the symmetry to P-6.

Structural studies of cytochrome reductase: Improved membrane crystals of the enzyme complex and crystallization of a subcomplex

Membrane crystals of mitochondrial ubiquinol: cytochrome c reductase of improved size and long-range order and of the cytochrome bc1 subcomplex have been obtained by a dialysis method. The enzyme--Triton X-100 complex was mixed with Triton phospholipid micelles and the Triton slowly removed by dialysis for 48 hours at pH 5.5 at room temperature or above. The effect of varying the pH and temperature on the shape, size and order of the crystals is described.