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MAD
Terms modified by MAD Selected AbstractsAssessment of different techniques for subcutaneous glucose monitoring in Type 1 diabetic patients during ,real-life' glucose excursionsDIABETIC MEDICINE, Issue 3 2010J. K. Mader Diabet. Med. 27, 332,338 (2010) Abstract Aims, To compare the accuracy of two marketed subcutaneous glucose monitoring devices (Guardian RT, GRT; GlucoDay S, GDS) and standard microdialysis (CMA60; MD) in Type 1 diabetic patients. Methods, Seven male Type diabetic patients were investigated over a period of 26 h simulating real-life meal glucose excursions. Catheters of the three systems were inserted into subcutaneous adipose tissue of the abdominal region. For MD, interstitial fluid was sampled at 30- to 60-min intervals for offline glucose determination. Reference samples were taken at 15- to 60-min intervals. All three systems were prospectively calibrated to reference. Median differences, median absolute relative differences (MARD), median absolute differences (MAD), Bland,Altman plot and Clark Error Grid were used to determine accuracy. Results, Bland,Altman analysis indicated a mean glucose difference (2 standard deviations) between reference and interstitial glucose of ,10.5 (41.8) % for GRT, 20.2 (55.9) % for GDS and 6.5 (35.2) % for MD, respectively. Overall MAD (interquartile range) was 1.07 (0.39; 2.04) mmol/l for GRT, 1.59 (0.54; 3.08) mmol/l for GDS and 0.76 (0.26; 1.58) mmol/l for MD. Overall MARD was 15.0 (5.6; 23.4) % (GRT), 19.7 (6.1; 37.6) % (GDS) and 8.7 (4.1; 18.3) % (MD), respectively. Total sensor failure occurred in two subjects using GRT and one subject using GDS. Conclusions, The three investigated technologies had comparable performance. Whereas GRT underestimated actual blood glucose, GDS and MD overestimated blood glucose. Considerable deviations during daily life meal glucose excursions from reference glucose were observed for all three investigated technologies. Present technologies may require further improvement until individual data can lead to direct and automated generation of therapeutic advice in diabetes management. [source] The Modified Atkins DietEPILEPSIA, Issue 2008Eric H. Kossoff Summary In 2003, a case series was published describing the benefits of a less restrictive ketogenic diet (KD) started as an outpatient without a fast and without any restrictions on calories, fluids, or protein. This "Modified Atkins Diet" (MAD) restricts carbohydrates to 10 g/day (15 g/day in adults) while encouraging high fat foods. Now 5 years later, there have been eight prospective and retrospective studies published on this alternative dietary therapy, both in children as well as adults. In these reports, 45 (45%) have had 50,90% seizure reduction, and 28 (28%) >90% seizure reduction, which is remarkably similar to the traditional KD. This review will discuss basics and tips to best provide the MAD, evidence for its efficacy, suggestions about the role of ketosis in dietary treatment efficacy, and its side effect profile. Lastly, the possible future benefits of this treatment for new-onset seizures, adults, neurologic conditions other than epilepsy, and developing countries of the world will be discussed. [source] Structures of Four Crystal Forms of DecaplaninHELVETICA CHIMICA ACTA, Issue 5 2003Christopher Lehmann The glycopeptide antibiotic decaplanin (1; formerly known as MM 47761 and M86-1410) crystallizes in two P21 and two P6122 crystal forms, each with four monomers in the asymmetric unit, with solvent contents varying from 48 to 69%. Although with ca. 600 unique atoms, the structures are larger than typical small molecules, one was solved by direct methods. The other three were solved by typical macromolecular methods: single-wavelength anomalous diffraction (SAD) of the Cl-atoms present naturally in the structure, multiple-wavelength anomalous diffraction (MAD) at the Br absorption edge for a crystal soaked in NaBr solution, and molecular replacement. There is evidence of appreciable radiation damage with loss of 20,30% of the covalent and ionic halogens affecting the synchrotron datasets that may even have unintentionally facilitated the MAD structure solution. The structures contain the dimer units typical of antibiotics related to vancomycin, but, in addition, there are a variety of further intermolecular interactions responsible for the polymorphy leading to intertwined 61 -helices in two of the crystal forms. Except for the sugars and some sidechains, the conformations of the 16 independent monomers are very similar. [source] Comorbidity and mixed anxiety-depressive disorder: clinical curiosity or pathophysiological need?HUMAN PSYCHOPHARMACOLOGY: CLINICAL AND EXPERIMENTAL, Issue S1 2001Hans-Ulrich Wittchen Abstract The paper reviews available epidemiological evidence for the existence of and the implications of comorbidity of anxiety and depressive disorders and mixed anxiety,depressive (MAD) disorders. Using epidemiolological evidence of prevalence and incidence and data relating to time-course of illness, risk factor and outcome, it is concluded: (1) that anxiety,depression comorbidity is quite frequent in epidemiological and clinical settings throughout the world; (2) this comorbidity is diagnosis-specific and is associated with increased vulnerabilities and risks as well as poorer outcome and marked disabilities; and (3) no such evidence was found for MAD disorders. Contrary to what was predicted, the prevalence of MAD disorders was quite low even when using the more recent criteria of the Diagnostic and Statistical Manual of Mental Disorders, 4th edition. (4) Furthermore, there was quite a heterogeneous pattern in terms of risk, severity and outcome making it questionable whether this disorder, as currently defined, is a clinical entity. These findings are discussed in terms of two perspectives, the ,lumpers' with their dimensional view and the ,splitters' with their categorical view. It is concluded that although comorbidity of threshold anxiety and depressive disorders seems to be an important phenomenon, no such evidence is provided for MAD disorders. Copyright © 2001 John Wiley & Sons, Ltd. [source] Manual superscaffolding of honey bee (Apis mellifera) chromosomes 12,16: implications for the draft genome assembly version 4, gene annotation, and chromosome structureINSECT MOLECULAR BIOLOGY, Issue 4 2007Hugh M. Robertson Abstract The euchromatic arms of the five smallest telocentric chromosomes in the honey bee genome draft Assembly v4 were manually connected into superscaffolds. This effort reduced chromosomes 12,16 from 30, 21, 25, 42, and 21 mapped scaffolds to five, four, five, six, and five superscaffolds, respectively, and incorporated 178 unmapped contigs and scaffolds totalling 2.6 Mb, a 6.4% increase in length. The superscaffolds extend from the genetically mapped location of the centromere to their identified distal telomeres on the long arms. Only two major misassemblies of 146 kb and 65 kb sections were identified in this 23% of the mapped assembly. Nine duplicate gene models on chromosomes 15 and 16 were made redundant, while another 15 gene models were improved, most spectacularly the MAD (MAX dimerization protein) gene which extends across 11 scaffolds for at least 400 kb. [source] Improved Accountability Disclosures by Canadian Universities,ACCOUNTING PERSPECTIVES, Issue 1 2003MORTON NELSON ABSTRACT Canadian university disclosures have been tracked from 1988 to 2000 using the modified accountability disclosure (MAD) index developed by Coy, Dixon, and Tower (1993) and Coy, Tower, and Dixon (1993) in their study of New Zealand universities. During the first eight years of the period under investigation, there was very little change in accountability disclosures. However, for the periods ending in 1997 through 2000, there has been a statistically significant annual improvement. This paper examines the reasons for these changes as indicated in the interviews with the presidents, or their designates, of Canadian universities. Factors include increased fund raising by the universities and pressures by the public and governments for universities to become more accountable, while a change in accounting pronouncements appears to have had little effect. [source] Real Options Analysis: Where Are the Emperor's Clothes?JOURNAL OF APPLIED CORPORATE FINANCE, Issue 2 2005Adam Borison Once a topic of interest only to finance specialists, real options analysis now receives active, mainstream attention in business schools and industry. This article provides practitioners with a critical review of five well-established real options approaches that are extensively documented in the academic and professional literature. These approaches include the "classic approach" and "revised classic approach" (as proposed by Martha Amram and Nalin Kulatilaka), the "subjective approach" (as proposed by Tim Luehrman), the "MAD Approach" (as proposed by Tom Copeland and Vladimir Antikarov), and the "integrated approach" (as proposed by James Smith and Robert Nau). The article discusses the assumptions, mechanics, and potential range of applications of each approach, along with the results when applied to a simple case involving development of a natural gas field. While the approaches share a focus on investment flexibility and shareholder value, they rely on fundamentally different assumptions, use significantly different techniques, and can produce dramatically different results. Consequently, a great deal of thought must go into selecting and applying them in practice. The revised classic approach appears to be best suited to cases dominated either by "market" risk or "private" risk alone, and where approximate results are acceptable and resources are limited. The integrated approach is best suited to cases with a mix of market and technological risks, and where accuracy and a management roadmap are critical. [source] The revenge of the Patterson methods.JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2007The Patterson techniques, recently developed by the same authors for the ab initio crystal structure solution of proteins, have been applied to single and multiple anomalous diffraction (SAD and MAD) data to find the substructure of the anomalous scatterers. An automatic procedure has been applied to a large set of test structures, some of which were originally solved with remarkable difficulty. In all cases, the procedure automatically leads to interpretable electron density maps. Patterson techniques have been compared with direct methods; the former seem to be more efficient than the latter, so confirming the results obtained for ab initio phasing, and disproving the common belief that they could only be applied to determine large equal-atom substructures with difficulty. [source] Phasing possibilities using different wavelengths with a xenon derivativeJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2002Santosh Panjikar Xenon derivatives are generally expected to be isomorphous with the native; however, the K - and L -absorption edges are not easily accessible on most synchrotron beamlines, which might limit their usefulness in phase determination. Various phasing procedures for xenon-derivatized porcine pancreatic elastase have been investigated using data sets measured at three generally accessible wavelengths. The importance of highly redundant data in measuring precise anomalous differences is highlighted and it is shown that, after such measurements, a single isomorphous replacement anomalous scattering (SIRAS) procedure yields a better phase set than those generated by single anomalous scattering (SAS) or multiwavelength anomalous diffraction (MAD) procedures. [source] Determination of rank by median absolute deviation (DRMAD): a simple method for determining the number of principal factors responsible for a data matrix,JOURNAL OF CHEMOMETRICS, Issue 1 2009Edmund R. Malinowski Abstract Median absolute deviation (MAD) is a well-established statistical method for determining outliers. This simple statistic can be used to determine the number of principal factors responsible for a data matrix by direct application to the residual standard deviation (RSD) obtained from principal component analysis (PCA). Unlike many other popular methods the proposed method, called determination of rank by MAD (DRMAD), does not involve the use of pseudo degrees of freedom, pseudo F -tests, extensive calibration tables, time-consuming iterations, nor empirical procedures. The method does not require strict adherence to normal distributions of experimental uncertainties. The computations are direct, simple to use and extremely fast, ideally suitable for online data processing. The results obtained using various sets of chemical data previously reported in the chemical literature agree with the early work. Limitations of the method, determined from model data, are discussed. An algorithm, written in MATLAB format, is presented in the Appendix. Copyright © 2008 John Wiley & Sons, Ltd. [source] Short-term effects of a mandibular advancement device on obstructive sleep apnoea: an open-label pilot trialJOURNAL OF ORAL REHABILITATION, Issue 8 2005G. AARAB summary, Obstructive sleep apnoea (OSA) is a common sleep disorder, which is, among others, associated with snoring. OSA has a considerable impact on a patient's general health and daily life. Nasal continuous positive airway pressure (nCPAP) is frequently used as a ,gold standard' treatment for OSA. As an alternative, especially for mild/moderate cases, mandibular advancement devices (MADs) are prescribed increasingly. Their efficacy and effectiveness seem to be acceptable. Although some randomized clinical trials (RCTs) have been published recently, most studies so far are case studies. Therefore, our department is planning a controlled RCT, in which MADs are compared with both nCPAP and a control condition in a parallel design. As a first step, an adjustable MAD was developed with a small, more or less constant vertical dimension at different mandibular positions. To test the device and the experimental procedures, a pilot trial was performed with 10 OSA patients (six mild, four moderate; one women, nine men; mean age = 47·9 ± 9·7 years). They all underwent a polysomnographic recording before as well as 2,14 weeks after insertion of the MAD (adjusted at 50% of the maximal protrusion). The apnoea,hypopnoea index (AHI) was significantly reduced with the MAD in situ (P = 0·017). When analysed as separate groups, the moderate cases showed a significantly larger decrease in AHI than the mild cases (P = 0·012). It was therefore concluded from this pilot study that this MAD might be an effective tool in the treatment of, especially, moderate OSA. [source] Overview and new developments in softer X-ray (2Å < , < 5Å) protein crystallographyJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004John R. Helliwell New methodologies with synchrotron radiation and X-ray free electron lasers (XFELs) in structural biology are being developed. Recent trends in harnessing softer X-rays in protein crystallography for phase determination are described. These include reference to a data-collection test at 2.6 Å wavelength with a lysozyme crystal on SRS station 7.2 (Helliwell, 1983) and also use of softer X-rays (2,Å wavelength) to optimise f," at the xenon L1 absorption edge in the Single Isomorphous Replacement Optimised Anomalous Scattering ('SIROAS') structure determination of apocrustacyanin A1 with four, partially occupied, xenon atoms (Cianci et al., 2001; Chayen et al., 2000). The hand of the protein was determined using the f," enhanced sulphur anomalous signal from six disulphides in the protein dimer of 40,kDa. In a follow-up study the single wavelength xenon L1 -edge f," optimised data set alone was used for phase determination and phase improvement by solvent flattening etc. (CCP4 DM) (Olczak et al., 2003). Auto-tracing of the protein was feasible but required additional diffraction data at higher resolution. This latter could be avoided in future by using improved tilted detector settings during use of softer X-rays, i.e. towards back-scattering recording (Helliwell, 2002). The Olczak et al. study has already led to optimisation of the new SRS beamline MPW,MAD,10 (see www.nwsgc.ac.uk) firstly involving the thinning of the beryllium windows as much as possible and planning for a MAR Research tilted detector `desk top beamline' geometry. Thus the use of softer, i.e. 2 to 3,Å wavelength range, X-rays will allow optimisation of xenon and iodine L -edge f," and enhancing of sulphur f," signals for higher throughput protein crystallography. Softer X-rays utilisation in protein crystallography includes work done on SRS bending-magnet station 7.2 in the early 1980s by the author as station scientist (Helliwell, 1984). In the future development of XFELs these softer X-ray wavelengths could also be harnessed and relax the demands to some extent on the complexity and cost of an XFEL. Thus, by use of say 4,Å XFEL radiation and use of a back-scattering geometry area detector the single molecule molecular transform could be sampled to a spatial resolution of 2,Å, sufficient, in principle, for protein model refinement (Miao et al., 1999). Meanwhile, Miao et al. (2003) report the first experimental recording of the diffraction pattern from intact Escherichia coli bacteria using coherent X-rays, with a wavelength of 2,Å, at a resolution of 30,nm and a real-space image constructed. The new single-particle X-ray diffraction-imaging era has commenced. [source] MAD techniques applied to powder data: finding the structure given the substructureACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Angela Altomare The joint probability distribution function method is applied to multiple-wavelength anomalous dispersion (MAD) powder data. The distributions are calculated by assuming prior knowledge of the scattering intensities at two wavelengths and of the anomalous-scatterer substructure. The method leads to formulas estimating the full structure phases and their reliability. The procedure has been applied to two structures, one unknown and one known; the second was used as a control for the phasing procedure. In spite of the unavoidable peak overlapping in the diffraction pattern, the formulas proved to be very effective. Combined with a new algorithm for phase extension, they enabled the solution of both crystal structures. [source] The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 Å resolution,a putative transcription factorPROTEIN SCIENCE, Issue 3 2007Edyta A.L. Sieminska Abstract The structure of the PA1607 protein from Pseudomonas aureginosa was determined at 1.85 Å resolution using the Se-Met multiwavelength anomalous diffraction (MAD) technique. PA1607 forms a dimer and adopts a winged-helix motif similar to the MarR family of transcription regulators, though it has an unusual dimerization profile. The DNA-binding regions and a putative metal-binding site are not conserved in PA1607. [source] Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Å resolutionPROTEIN SCIENCE, Issue 7 2005Ryoichi Arai Abstract The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER homolog (ERH) is highly conserved among vertebrates, invertebrates, and plants. Xenopus laevis ERH was reported to be a transcriptional repressor. Here we report the 2.1 Å crystal structure of murine ERH (Protein Data Bank ID 1WZ7), determined by the multiwavelength anomalous dispersion (MAD) method. The monomeric structure of ERH comprises a single domain consisting of three ,-helices and four ,-strands, which is a novel fold. In the crystal structure, ERH assumes a dimeric structure, through interactions between the ,-sheet regions. The formation of an ERH dimer is consistent with the results of analytical ultracentrifugation. The residues at the core region and at the dimer interface are highly conserved, suggesting the conservation of the dimer formation as well as the monomer fold. The long flexible loop (44,53) is also significantly conserved, suggesting that this loop region may be important for the functions of ERH. In addition, the putative phosphorylation sites are located at the start of the ,2-strand (Thr18) and at the start of the ,1-helix (Ser24), implying that the phosphorylation might cause some structural changes. [source] Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8PROTEIN SCIENCE, Issue 11 2004Mutsuko Kukimoto-Niino Abstract TT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of TT1887 and TT1465 at 1.8 Å and 2.2 Å resolutions, respectively, as determined by the multiwavelength anomalous dispersion (MAD) method. TT1887 is a homotetramer, while TT1465 is a homohexamer in the crystal and in solution. The structures of the TT1887 and TT1465 monomers contain single domains with the Rossmann fold, comprising six , helices and seven , strands, and are quite similar to each other. The major structural differences exist in the N terminus of TT1465, where there are two additional , helices. A comparison of the structures revealed the elements that are responsible for the different oligomerization modes. The distributions of the electrostatic potential on the solvent-accessible surfaces suggested putative active sites. [source] Crystal structure of E. coli ,,carbonic anhydrase, an enzyme with an unusual pH,dependent activityPROTEIN SCIENCE, Issue 5 2001Jeff D. Cronk CA, carbonic anhydrase; ECCA, Escherichia coli ,-carbonic anhydrase; PPCA, Porphyridium purpureum ,-carbonic anhydrase; PSCA, Pisum sativum ,-carbonic anhydrase; EXAFS, extended X-ray absorption fine structure spectroscopy; MAD, multiwavelength anomalous dispersion Abstract Carbonic anhydrases fall into three distinct evolutionary and structural classes: ,, ,, and ,. The ,-class carbonic anhydrases (,-CAs) are widely distributed among higher plants, simple eukaryotes, eubacteria, and archaea. We have determined the crystal structure of ECCA, a ,-CA from Escherichia coli, to a resolution of 2.0 Å. In agreement with the structure of the ,-CA from the chloroplast of the red alga Porphyridium purpureum, the active-site zinc in ECCA is tetrahedrally coordinated by the side chains of four conserved residues. These results confirm the observation of a unique pattern of zinc ligation in at least some ,-CAs. The absence of a water molecule in the inner coordination sphere is inconsistent with known mechanisms of CA activity. ECCA activity is highly pH-dependent in the physiological range, and its expression in yeast complements an oxygen-sensitive phenotype displayed by a ,-CA-deletion strain. The structural and biochemical characterizations of ECCA presented here and the comparisons with other ,-CA structures suggest that ECCA can adopt two distinct conformations displaying widely divergent catalytic rates. [source] Does the MAD system make test facilities mad?QUALITY ASSURANCE JOURNAL, Issue 4 2006V. Amalan Stanley Abstract There needs more clarity in ad hoc Good Laboratory Practice (GLP) certification conferred to test facilities of non-member economies. There is a similar kind of issue with the ,GLP status' of the test data generated by a test facility that has been conferred GLP certification by the country that is only a provisional adherent. In both cases, the objective of the Mutual Acceptance of Data (MAD) system will not be fulfilled if the answer is ,no'. Copyright © 2006 John Wiley & Sons, Ltd. [source] Tales Calculated to Drive You MAD": The Debunking of Spies, Superheroes, and Cold War Rhetoric in Mad Magazine's "SPY vs SPY"THE JOURNAL OF POPULAR CULTURE, Issue 1 2007TEODORA CARABAS First page of article [source] Emerging Chinese Architectural Practice Under Development: MADA s.p.a.m., URBANUS Architecture & Design, Atelier Zhanglei, standardarchitecture, MADARCHITECTURAL DESIGN, Issue 5 2008Laurence Liauw Abstract China presents unique opportunities to design and build innovative architectural structures. Laurence Liauw showcases five nascent practices, still under development, MADA s.p.a.m.,URBANUS, Atelier Zhanglei, standardarchitecture and MAD - who after having gained educations at top institutions in the US and Europe have come home to build cutting-edge designs that harness new technologies, creative processes and critical thinking. Copyright © 2008 John Wiley & Sons, Ltd. [source] Selenium incorporation using recombinant techniquesACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Helen Walden Using selenomethionine to phase macromolecular structures is common practice in structure determination, along with the use of selenocysteine. Selenium is consequently the most commonly used heavy atom for MAD. In addition to the well established recombinant techniques for the incorporation of selenium in prokaryal expression systems, there have been recent advances in selenium labelling in eukaryal expression, which will be discussed. Tips and things to consider for the purification and crystallization of seleno-labelled proteins are also included. [source] The magic triangle goes MAD: experimental phasing with a bromine derivativeACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Tobias Beck Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br,K edge was successfully carried out. Radiation damage to the bromine,carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out. [source] Experimental phasing with SHELXC/D/E: combining chain tracing with density modificationACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010George M. Sheldrick The programs SHELXC, SHELXD and SHELXE are designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXE by the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue ,-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a `no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap. [source] ACORN2: new developments of the ACORN conceptACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009E. J. Dodson The density-modification procedures incorporated in ACORN, available in the CCP4 package, have proved to be very successful in solving and refining high-resolution crystal structures from very poor starting sets. These can be calculated from a correctly positioned initial fragment containing between 1 and 8% of the scattering power of the total structure. Improvements of ACORN, reported here and incorporated in the program ACORN2, have lowered the size of the fragment required and examples are given of structures solved with only 0.25% of the scattering power in the fragment, which may be a single atom. Applications of ACORN2 to structures with space group P1 have shown the remarkable property that when the starting point is a pair of equal atoms, or even a single atom placed at the origin, the refinement process breaks the centric nature of the initial phases and converges to phases corresponding to one of the two possible enantiomorphs. Examples are given of the application of ACORN2 to the solution and/or refinement of a number of known trial structures and to the refinement of structures when phases are available either from MAD or from a molecular-replacement model. [source] Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizardACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Thomas C. Terwilliger Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skewness of electron density with the local correlation of r.m.s. density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol wizard carries out automated structure solution based on any combination of SAD, MAD, SIR or MIR data sets. The wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing. [source] Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2008Mark Andrew White Human cytochrome P450 46A1 (CYP46A1) is one of the key enzymes in cholesterol homeostasis in the brain. The crystallization and heavy-atom structure solution of an active truncated CYP46A1 in complex with the high-affinity substrate analogue cholesterol-3-sulfate (CH-3S) is reported. The 2.6,Å structure of CYP46A1,CH-3S was solved using both anion and cation heavy-atom salts. In addition to the native anomalous signal from the haem iron, an NaI anion halide salt derivative and a complementary CsCl alkali-metal cation salt derivative were used. The general implications of the use of halide and alkali-metal quick soaks are discussed. The importance of using isoionic strength buffers, the titration of heavy-atom salts into different ionic species and the role of concentration are considered. It was observed that cation/anion-binding sites will occasionally overlap, which could negatively impact upon mixed RbBr soaks used for multiple anomalous scatterer MAD (MMAD). The use of complementary cation and anion heavy-atom salt derivatives is a convenient and powerful tool for MIR(AS) structure solution. [source] MAD phasing using the (Ta6Br12)2+ cluster: a retrospective studyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2008Oliwia Pasternak The crystal structure of cytokinin-specific binding protein (CSBP) containing four independent molecules with 4 × 155 = 620 residues in the asymmetric unit of the P64 unit cell has been solved by three-wavelength MAD using 1.8,Å resolution data recorded from a crystal derivatized with the dodecabromohexatantalum cation (Ta6Br12)2+. The diffraction data contained a very strong anomalous signal (allowing successful phasing even using peak SAD data alone) despite the fact that the five (Ta6Br12)2+ clusters found in the asymmetric unit have low occupancy (about 0.3). The derivative structure has been successfully refined to R = 0.158, providing interesting details on the geometry of the (Ta6Br12)2+ cluster, its interactions with the protein and on the backsoaking of a cytokinin ligand that was originally part of a CSBP,cytokinin complex in the native crystals used for (Ta6Br12)2+ derivatization. A simulation analysis of the phasing power of the (Ta6Br12)2+ ions at artificially imposed resolution limits shows that it is not possible to resolve the individual Ta atoms if the dmin limit of the data is higher than 2.9,Å. Additionally, for successful Ta identification the (Ta6Br12)2+ complex should be specifically bound and ordered. Good binding at the protein surface is facilitated by the presence of acidic groups, indicating higher pH buffer conditions to be preferable. In addition, the water channels in the crystal should be sufficiently wide (at least 11,Å) to allow free diffusion of the (Ta6Br12)2+ ions on soaking. A retrospective look at the initial molecular-replacement calculations provides interesting insights into how the peculiar packing mode and strong bias of the molecular-replacement-phased electron-density maps had hindered successful solution of the structure by this method. [source] Structure of inorganic pyrophosphatase from Helicobacter pyloriACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2005Chun Ai Wu Inorganic pyrophosphatase (PPase) is a ubiquitous cytosolic enzyme which catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to orthophosphate (Pi). The crystal structure of inorganic pyrophosphatase from Helicobacter pylori (H-PPase) has been solved by MAD and refined to an R factor of 20.6% at 2.6,Å resolution. The crystallographic asymmetric unit contains a homohexameric H-PPase arranged as a dimer of trimers. While most of the structural elements of PPases are highly conserved in H-PPase, some unique structural features are localized in the flexible loops near the active site, suggesting that the structural flexibility of these loops is required for the catalytic efficiency of PPase. [source] Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structureACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2005Thomas R. M. Barends Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15,Å resolution. When phasing with molecular replacement using the native structure failed, selenium MAD was used to obtain initial phases. However, after MAD phasing the crystals were found to be tetartohedrally twinned, hampering correct space-group determination and refinement. A refinement protocol was designed to take tetartohedral twinning into account and was successfully applied to refine the structure. The refinement protocol is described and the reasons for the failure of molecular replacement and the success of MAD are discussed in terms of the effects of the tetartohedral twinning. [source] Crystallization of FLINC4, an intramolecular LMO4,ldb1 complexACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003Janet E. Deane LMO4 is the most recently discovered member of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO4 is comprised primarily of two tandemly repeated LIM domains and interacts with the ubiquitous nuclear adaptor protein ldb1. This interaction is mediated via the LIM domains of LMO4 and the LIM-interaction domain (LID) of ldb1. An intramolecular complex, termed FLINC4, consisting of the two LIM domains from LMO4 linked to the LID domain of ldb1 via a flexible linker has been engineered, purified and crystallized. The trigonal crystals, which belong to space group P312 with unit-cell parameters a = 61.3, c = 93.2,Å, diffract to 1.3,Å resolution and contain one molecule of FLINC4 per asymmetric unit. Native and multiple-wavelength anomalous dispersion (MAD) data collected at the Zn X-ray absorption edge have been recorded to 1.3 and 1.7,Å resolution, respectively. Anomalous Patterson maps calculated with data collected at the peak wavelength show strong peaks sufficient to determine the positions of four Zn atoms per asymmetric unit. [source] | ||||||||||||||||||||||||||||||||||||||||