{"title":"Macromolecular applications of SHELX","authors":"G. Sheldrick","doi":"10.1107/97809553602060000863","DOIUrl":"https://doi.org/10.1107/97809553602060000863","url":null,"abstract":"The SHELX system for small-molecule crystallography dates back to the early 1970s. The current refinement program, SHELXL97, is also useful for high-resolution macromolecular refinement. SHELXC, D and E are more recent additions for experimental phasing using single-wavelength anomalous dispersion (SAD), single isomorphous replacement (SIR), combined SAD and SIR (SIRAS), multi-wavelength anomalous dispersion (MAD) and radiation-damage-induced phasing (RIP) data. They are fast and simple to use, and in favourable cases produce high-quality maps despite very weak initial phase information. \u0000 \u0000 \u0000Keywords: \u0000 \u0000SHELX; \u0000SHELXC; \u0000SHELXD; \u0000SHELXE; \u0000SHELXL; \u0000refinement; \u0000experimental phasing; \u0000substructure solution; \u0000density modification; \u0000autotracing","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123083610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 22.3 Hydrogen bonding in biological macromolecules","authors":"E. Baker","doi":"10.1107/97809553602060000887","DOIUrl":"https://doi.org/10.1107/97809553602060000887","url":null,"abstract":"Hydrogen bonds are weak non-covalent interactions, but their directional nature and the large number of hydrogen-bonding groups mean that they play a critical role in the structure and function of proteins and nucleic acids. Analyses of three-dimensional structures, particularly of proteins, reveal many consistent patterns, which are described in this review. Protein structures show almost complete saturation of hydrogen-bonding potential. Helices, β-strands, β-turns and γ-turns all show characteristic C=O···HN geometries, with helices having a variety of termination patterns. Local interactions are very common for main-chain···side-chain hydrogen bonds and may help direct protein folding. Non-local interactions, although fewer in number, can be very important for structural stability, and bound water molecules, because of their double-donor, double-acceptor capability, can play critical roles in satisfying overall hydrogen-bonding requirements. Finally, there is also a growing realization that non-conventional hydrogen bonds may play a more important role than hitherto recognized. \u0000 \u0000 \u0000Keywords: \u0000 \u0000beta-sheets; \u0000amino-aromatic hydrogen bonding; \u0000DNA; \u0000helices; \u0000hydrogen bonding; \u0000hydrogen-bonding criteria; \u0000hydrogen-bonding potential; \u0000nucleic acids; \u0000protein folding; \u0000protein stability; \u0000RNA; \u0000secondary structure; \u0000side-chain hydrogen bonding; \u0000turns","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117058521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparison of X‐ray detectors","authors":"S. Gruner, E. Eikenberry, M. Tate","doi":"10.1107/97809553602060000820","DOIUrl":"https://doi.org/10.1107/97809553602060000820","url":null,"abstract":"In this chapter, types of crystallographic X-ray detectors in common use, and several under development, are listed and their salient features are summarized. Detector characteristics of particular importance to crystallography include the detective quantum efficiency, spatial resolution, stopping power, dynamic range, and issues relating to calibration and reproducibility. These characteristics are discussed for different types of detectors and simple tests are described that can be used to evaluate detector performance. \u0000 \u0000 \u0000Keywords: \u0000 \u0000area detectors; \u0000detectors; \u0000photon-counting X-ray detectors; \u0000photon-integrating X-ray detectors; \u0000point X-ray detectors; \u0000X-ray detectors","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116412098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Wodak, A. Vagin, J. Richelle, U. Das, J. Pontius, H. Berman
{"title":"Chapter 21.2 Assessing the quality of macromolecular structures","authors":"S. Wodak, A. Vagin, J. Richelle, U. Das, J. Pontius, H. Berman","doi":"10.1107/97809553602060000880","DOIUrl":"https://doi.org/10.1107/97809553602060000880","url":null,"abstract":"In this chapter, an overview is presented of the different types of validation procedures applied to proteins and nucleic acids. An approach to model validation based on atomic volumes embodied in the program PROVE is illustrated in some detail and the package SFCHECK, which combines a set of criteria for evaluating the quality of the experimental data and the agreement of the model with the data, is described. \u0000 \u0000 \u0000Keywords: \u0000 \u0000SFCHECK; \u0000atomic resolution; \u0000coordinate errors; \u0000environment profiles; \u0000errors; \u0000knowledge-based interaction potentials; \u0000scaling; \u0000standard atomic volumes; \u0000structure validation","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121368583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 22.5 The relevance of the Cambridge Structural Database in protein crystallography","authors":"F. Allen, J. Cole, M. Verdonk","doi":"10.1107/97809553602060000889","DOIUrl":"https://doi.org/10.1107/97809553602060000889","url":null,"abstract":"The importance of high-resolution crystal structure data of small molecules to protein crystallography is highlighted. Specific areas covered include: mean molecular dimensions for peptidic fragments and other biologically important substructures, conformational information, hydrogen-bond geometries and their directionality, and other strong non-covalent interactions. The value of the IsoStar knowledge base of intermolecular interactions, derived from the CSD and from protein–ligand complexes in the PDB, is illustrated. The value of structural information from small molecules to our understanding of protein–ligand binding is also discussed, together with examples of how this information is important in the prediction of ligand binding modes and in software tools for protein–ligand docking. \u0000 \u0000 \u0000Keywords: \u0000 \u0000Cambridge Structural Database; \u0000databases; \u0000hydrogen bonding; \u0000intermolecular interactions; \u0000IsoStar; \u0000metal coordination geometry; \u0000nonbonded interactions; \u0000Protein Data Bank; \u0000protein–ligand interactions; \u0000structure validation; \u0000van der Waals radii","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132133770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Protein geometry: volumes, areas and distances","authors":"M. Gerstein, F. Richards","doi":"10.1107/97809553602060000885","DOIUrl":"https://doi.org/10.1107/97809553602060000885","url":null,"abstract":"In this chapter, methods for the calculation of the volumes and areas of proteins are surveyed. The application of Voronoi polyhedra to the calculation of volumes is focused on, with a discussion of how this construction is made and various aspects of it, including the calculation of standard sets of protein volumes. Various measures for protein surface areas, including the accessible surface area, are also discussed. \u0000 \u0000 \u0000Keywords: \u0000 \u0000molecular surface; \u0000molecular volumes; \u0000surface areas; \u0000surface-area calculation; \u0000surfaces; \u0000Voronoi construction; \u0000Voronoi polyhedra","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"150 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132288182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Introduction to cryocrystallography","authors":"H. Hope, S. Parkin","doi":"10.1107/97809553602060000827","DOIUrl":"https://doi.org/10.1107/97809553602060000827","url":null,"abstract":"A general introduction to cryocrystallography is provided. The chapter covers crystal mounting, cooling of biocrystals, principles of cooling equipment and frost prevention. Operational considerations, such as dual-stream instruments, electrically heated nozzles, temperature calibration and transfer of crystals to difractometers, are also described.","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"270 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114332860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular surfaces: calculations, uses and representations","authors":"M. S. Chapman, M. L. Connolly","doi":"10.1107/97809553602060000886","DOIUrl":"https://doi.org/10.1107/97809553602060000886","url":null,"abstract":"In this chapter, the calculation of molecular surface areas, the uses of surface-area calculations and the representation of molecular surfaces are discussed. \u0000 \u0000 \u0000Keywords: \u0000 \u0000GRASP; \u0000molecular surfaces; \u0000surface areas; \u0000representation of surfaces; \u0000surface-area calculation","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114958313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Expression and purification of membrane proteins for structural studies","authors":"J. Ernst, D. Yansura, C. Koth","doi":"10.1107/97809553602060000811","DOIUrl":"https://doi.org/10.1107/97809553602060000811","url":null,"abstract":"Despite the fact that over 200 unique membrane-protein structures have now been solved, significant challenges remain at all stages of protein production for both structural and functional studies. First, recombinant expression levels of membrane proteins are typically very low. Second, target proteins must be solubilized from their native environment, the cell membrane, and purified. This requires the use of detergents that can also cause the protein to denature or aggregate. Indeed, the repertoire of detergents that have been used successfully for membrane-protein structural studies is surprisingly limited. Third, obtaining well ordered crystals is often very difficult, even if milligramme quantities of high-quality membrane protein can be obtained. Despite these and other barriers, significant progress has been made over the last several years in determining the structures of members of many challenging membrane-protein families, including transporters, channels, intramembrane proteases and G-protein-coupled receptors. Based largely on these past successes, and analyses of recurrent trends, reasonable ‘first-pass’ strategies can now be proposed for most membrane-protein targets. Here, the current state of producing membrane proteins for structural studies is reviewed. An evidence-guided approach is detailed that should provide reasonable starting points for the production of many membrane-protein targets. \u0000 \u0000 \u0000Keywords: \u0000 \u0000membrane proteins; \u0000expression; \u0000purification; \u0000affinity tags","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"165 7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125968648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DM/DMMULTI software for phase improvement by density modification","authors":"K. Cowtan, K. Y. Zhang, P. Main","doi":"10.1107/97809553602060000849","DOIUrl":"https://doi.org/10.1107/97809553602060000849","url":null,"abstract":"The DM/DMMULTI software for phase improvement by density modification is described. \u0000 \u0000 \u0000Keywords: \u0000 \u0000DM/DMMULTI; \u0000density modification; \u0000phase improvement","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133752275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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