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Diffraction Data Analysis (diffraction + data_analysis)
Selected AbstractsDiffraction data analysis in the presence of radiation damageACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Dominika Borek In macromolecular crystallography, the acquisition of a complete set of diffraction intensities typically involves a high cumulative dose of X-ray radiation. In the process of data acquisition, the irradiated crystal lattice undergoes a broad range of chemical and physical changes. These result in the gradual decay of diffraction intensities, accompanied by changes in the macroscopic organization of crystal lattice order and by localized changes in electron density that, owing to complex radiation chemistry, are specific for a particular macromolecule. The decay of diffraction intensities is a well defined physical process that is fully correctable during scaling and merging analysis and therefore, while limiting the amount of diffraction, it has no other impact on phasing procedures. Specific chemical changes, which are variable even between different crystal forms of the same macromolecule, are more difficult to predict, describe and correct in data. Appearing during the process of data collection, they result in gradual changes in structure factors and therefore have profound consequences in phasing procedures. Examples of various combinations of radiation-induced changes are presented and various considerations pertinent to the determination of the best strategies for handling diffraction data analysis in representative situations are discussed. [source] Crystallization and preliminary crystallographic analysis of the central domain of Drosophila Dribble, a protein that is essential for ribosome biogenesisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Tat-Cheung Cheng Dribble (DBE) is a Drosophila protein that is essential for ribosome biogenesis. Bioinformatics analysis revealed a folded central domain of DBE which is flanked by structural disorder in the N- and C-terminal regions. The protein fragment spanning amino-acid residues 16,197 (DBE16,197) was produced for structural determination. In this report, the crystallization and preliminary X-ray diffraction data analysis of the DBE16,197 protein domain are described. Crystals of DBE16,197 were grown by the sitting-drop vapour-diffusion method at 289,K using ammonium phosphate as a precipitant. The crystals belonged to space group P212121. Data were collected that extended to beyond 2,Å resolution. [source] Crystallization and preliminary X-ray diffraction data analysis of stenodactylin, a highly toxic type 2 ribosome-inactivating protein from Adenia stenodactylaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Giovanna Tosi Ribosome-inactivating proteins (RIPs) inhibit protein synthesis and induce cell death by removing a single adenine from a specific rRNA loop. They can be divided into two main groups: type 1 and type 2 RIPs. Type 1 RIPs are single-chain enzymes with N-glycosidase activity. Type 2 RIPs contain two chains (A and B) linked by a disulfide bond. The A chain has RIP enzymatic activity, whereas the B chain shows lectin activity and is able to bind to glycosylated receptors on the cell surface. Stenodactylin is a type 2 RIP from the caudex of Adenia stenodactyla from the Passifloraceae family that has been recently purified and characterized. It shows a strong enzymatic activity towards several substrates and is more cytotoxic than other toxins of the same type. Here, the crystallization and preliminary X-ray diffraction data analysis of stenodactylin are reported. This RIP forms crystals that diffract to high resolution (up to 2.15,Å). The best data set was obtained by merging data collected from two crystals. Stenodactylin crystals belonged to the centred monoclinic space group C2 and contained two molecules in the asymmetric unit. [source] Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA elementACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Nithya Baburajendran The bone morphogenetic protein (BMP) signalling pathway regulates diverse processes such as cell differentiation, anterior/posterior axis specification, cell growth and the formation of extra-embryonic tissues. The transcription factor Smad1 relays the BMP signal from the cytoplasm to the nucleus, where it binds short DNA-sequence motifs and regulates gene expression. However, how Smad1 selectively targets particular genomic regions is poorly understood. In order to understand the physical basis of the specific interaction of Smad1 with DNA and to contrast it with the highly homologous but functionally distinct Smad3 protein, the DNA-binding Mad-homology 1 (MH1) domain of Smad1 was cocrystallized with a 17-mer palindromic Smad-binding element (SBE). The extensive optimizations of the length, binding-site spacing and terminal sequences of the DNA element in combination with the other crystallization parameters necessary for obtaining diffraction-quality crystals are described here. A 2.7,Å resolution native data set was collected at the National Synchrotron Radiation Research Centre, Taiwan, from crystals grown in a solution containing 0.2,M ammonium tartrate dibasic, 20% PEG 3350, 3% 2-propanol and 10% glycerol. The data set was indexed and merged in space group P222, with unit-cell parameters a = 73.94, b = 77.49, c = 83.78,Å, , = , = , = 90°. The solvent content in the unit cell is consistent with the presence of two Smad1 MH1 molecules bound to the duplex DNA in the asymmetric unit. [source] Crystallization and X-ray diffraction analysis of an `all-locked' nucleic acid duplex derived from a tRNASer microhelixACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Katja Behling Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called `locked nucleic acids' contain modified sugar moieties such as 2,- O,4,- C -methylene-bridged ,- d -ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA,DNA or LNA,RNA heteroduplexes has been well investigated, but the X-ray structure of an `all-locked' nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an `all-locked' nucleic acid helix, which was designed as an LNA originating from a tRNASer microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06,Å, , = 91.02°. A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9,Å resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48,Å3,Da,1 and a solvent content of 66.49% for the merged data. [source] Purification, crystallization and preliminary X-ray analysis of cytochrome P450 219A1 from Novosphingobium aromaticivorans DSM 12444ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Chuan Hong Cytochrome P450 enzymes catalyze a variety of reactions and are widely distributed in living organisms. In recent studies, the first members of five new families of cytochrome P450 enzymes have been identified, including cytochrome P450 219A1 (CYP219A1) from Novosphingobium aromaticivorans DSM 12444. It has also been reported that isolongifolen-9-one (C15H22O), a sesquiterpenoid ketone derivative, is a potential substrate for CYP219A1, inducing a ,95% shift of the haem spin state to high spin upon binding. The CYP219A1 protein has been crystallized and single crystals have been studied by X-ray crystallography. Diffraction data were collected to 2.4,Å resolution. The crystals belonged to space group P6, with unit-cell parameters a = 93.1, b = 93.1, c = 98.0,Å. Preliminary X-ray diffraction data analysis revealed that the asymmetric unit contained one protein molecule. [source] Expression, purification and preliminary X-ray diffraction studies of VERNALIZATION1208,341 from Arabidopsis thalianaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Gordon King VERNALIZATION1 (VRN1) is required in the model plant Arabidopsis thaliana for the epigenetic suppression of the floral repressor FLC by prolonged cold treatment. Stable suppression of FLC accelerates flowering, a physiological process known as vernalization. VRN1 is a 341-residue DNA-binding protein that contains two plant-specific B3 domains (B3a and B3b), a putative nuclear localization sequence (NLS) and two putative PEST domains. VRN1208,341 includes the second B3 domain and a region upstream that is highly conserved in the VRN1 orthologues of other dicotyledonous plants. VRN1208,341 was crystallized by the hanging-drop method in 0.05,M sodium acetate pH 6.0 containing 1.0,M NaCl and 18%(w/v) PEG 3350. Preliminary X-ray diffraction data analysis revealed that the VRN1208,341 crystal diffracted to 2.1,Å and belonged to space group C2, with unit-cell parameters a = 105.2, b = 47.9, c = 61.2,Å, , = 90.0, , = 115.4, , = 90.0°. Assuming that two molecules occupy the asymmetric unit, a Matthews coefficient of 2.05,Å3,Da,1 and a solvent content of 40.1% were calculated. [source] | ||||||||||