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Chapter 14.3 Automated MAD and MIR structure solution 第14.3章自动化MAD和MIR结构解决方案
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000846
T. Terwilliger, J. Berendzen
{"title":"Chapter 14.3 Automated MAD and MIR structure solution","authors":"T. Terwilliger, J. Berendzen","doi":"10.1107/97809553602060000846","DOIUrl":"https://doi.org/10.1107/97809553602060000846","url":null,"abstract":"In this chapter, the Solve software is described. Solve is designed to automate the solution of macromolecular X-ray structures in straightforward cases. The overall approach is to link together, in a seamless procedure, all the analysis steps that a crystallographer would normally carry out. In the process, the software converts each decision-making step into an optimization problem. A key element of the procedure is the scoring and ranking of possible solutions. For MAD data, a second key element is the conversion of MAD data to pseudo-SIRAS data, allowing for much faster structure solution. The automated procedure has been used to determine structures with as many as 56 selenium atoms in the asymmetric unit. \u0000 \u0000 \u0000Keywords: \u0000 \u0000Solve; \u0000anomalous-scatterer labels for MAD; \u0000anomalous scattering; \u0000anomalous scattering factors; \u0000automated structure solution for MAD and MIR; \u0000MAD; \u0000MIR; \u0000multiple isomorphous replacement; \u0000multiwavelength anomalous diffraction; \u0000phasing; \u0000scattering factors; \u0000structure solution","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"82 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":"124109409","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}
引用次数: 1
The TNT refinement package TNT改进包
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000861
D. Tronrud, L. T. Eyck
{"title":"The TNT refinement package","authors":"D. Tronrud, L. T. Eyck","doi":"10.1107/97809553602060000861","DOIUrl":"https://doi.org/10.1107/97809553602060000861","url":null,"abstract":"The TNT refinement package was created in the late 1970s and its development continued for about 25 years. Its design included many features not present in its contemporaries and allowed for the testing and addition of many novel tools during its lifespan. These include the implementation of stereochemical restraints to molecules in other asymmetric units (both bonded and non-bonded), space-group-optimized fast Fourier transforms, which allowed rapid crystallographic calculations, and a quick and easy method to model the scattering of bulk solvent, which allowed the use of low-resolution data in refinement. TNT is no longer being developed by its original authors but its code has been included in Global Phasing, Ltd's program Buster, where considerable improvements have been made.","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"13 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":"121955788","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}
引用次数: 1
Chapter 4.3 Application of protein engineering to enhance crystallizability and improve crystal properties 4.3应用蛋白质工程增强结晶性，改善晶体性能
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000814
Z. Derewenda
{"title":"Chapter 4.3 Application of protein engineering to enhance crystallizability and improve crystal properties","authors":"Z. Derewenda","doi":"10.1107/97809553602060000814","DOIUrl":"https://doi.org/10.1107/97809553602060000814","url":null,"abstract":"Until recently, protein crystallization has mostly been regarded as a stochastic event over which the investigator has little or no control. With the dramatic technological advances in synchrotron-radiation sources and detectors and the equally impressive progress in crystallographic software, including automated model building and validation, crystallization has increasingly become the rate-limiting step in X-ray diffraction studies of macromolecules. However, with the advent of recombinant methods it has also become possible to engineer target proteins and their complexes for higher propensity to form crystals with desirable X-ray diffraction qualities. As most proteins that are under investigation today are obtained by heterologous overexpression, these techniques hold the promise of becoming routine tools with the potential to transform classical crystallization screening into a more rational high-success-rate approach. This chapter presents an overview of protein-engineering methods designed to enhance crystallizability and discusses a number of examples of their successful application. \u0000 \u0000 \u0000Keywords: \u0000 \u0000protein engineering; \u0000protein crystallization; \u0000fusion proteins; \u0000crystallization chaperones; \u0000post-translational modifications; \u0000surface-entropy reduction","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"148 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":"114209922","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}
引用次数: 0
Molecular graphics and animation 分子图形和动画
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000854
A. Olson
{"title":"Molecular graphics and animation","authors":"A. Olson","doi":"10.1107/97809553602060000854","DOIUrl":"https://doi.org/10.1107/97809553602060000854","url":null,"abstract":"The use of molecular graphics and animation for the visualization of biological macromolecules is described. The topics covered include: the evolution of molecular graphics hardware and software; the representation and visualization of molecular data and models; and presentation graphics.","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"24 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":"124902149","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}
引用次数: 2
The Worldwide Protein Data Bank 世界蛋白质数据库
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000896
H. Berman, K. Henrick, G. Kleywegt, Haruki Nakamura, J. Markley
{"title":"The Worldwide Protein Data Bank","authors":"H. Berman, K. Henrick, G. Kleywegt, Haruki Nakamura, J. Markley","doi":"10.1107/97809553602060000896","DOIUrl":"https://doi.org/10.1107/97809553602060000896","url":null,"abstract":"The Protein Data Bank (PDB) is the single, freely available, global archive of structural data for biological macromolecules. It is maintained by the wwPDB consortium consisting of the Research Collaboratory for Structural Bioinformatics (RCSB PDB), the Protein Data Bank in Europe (PDBe), the PDB Japan (PDBj) and the BioMagResBank (BMRB). This chapter describes the organization of the wwPDB, the systems in place for data deposition, annotation and distribution, and a summary of the services provided by the wwPDB member sites. \u0000 \u0000 \u0000Keywords: \u0000 \u0000Protein Data Bank","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"1 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":"125783310","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}
引用次数: 48
Chapter 11.6 XDS 11.6 XDS
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000835
W. Kabsch
{"title":"Chapter 11.6 XDS","authors":"W. Kabsch","doi":"10.1107/97809553602060000835","DOIUrl":"https://doi.org/10.1107/97809553602060000835","url":null,"abstract":"The usage and control of recent modifications of the program package XDS for the processing of rotation images are described in the context of previous versions. New features include automatic determination of spot size and reflecting range, and recognition and assignment of crystal symmetry. Moreover, the limitations of earlier package versions on the number of correction/scaling factors and the representation of pixel contents have been removed. Large program parts have been restructured for parallel processing so that the quality and completeness of collected data can be assessed soon after measurement. \u0000 \u0000 \u0000Keywords: \u0000 \u0000XDS","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"89 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":"127188153","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}
引用次数: 0
PrimeX and the Schrödinger computational chemistry suite of programs PrimeX和Schrödinger计算化学套件程序
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000864
J. Bell, Yixiang X. Cao, J. Gunn, T. Day, Emilio Gallicchio, Zhiyong Zhou, R. Levy, R. Farid
{"title":"PrimeX and the Schrödinger computational chemistry suite of programs","authors":"J. Bell, Yixiang X. Cao, J. Gunn, T. Day, Emilio Gallicchio, Zhiyong Zhou, R. Levy, R. Farid","doi":"10.1107/97809553602060000864","DOIUrl":"https://doi.org/10.1107/97809553602060000864","url":null,"abstract":"PrimeX is a new X-ray crystal structure refinement program for biological macromolecules from Schrodinger, Inc. It produces an all-atom model at moderate resolution that is in excellent agreement with the diffraction data and that is also suitable for immediate use in computational chemistry applications. The program features maximum-likelihood reciprocal-space minimization, simulated-annealing refinement, ligand placement, loop building and side-chain placement. PrimeX is integrated with the powerful molecular-graphics program Maestro, which provides an easy-to-use graphical interface. Command-line access to PrimeX tools provides for their scripting into complex workflows. Additional information about these features and the methods used therein are presented. \u0000 \u0000 \u0000Keywords: \u0000 \u0000PrimeX; \u0000Glide; \u0000Prime; \u0000Maestro; \u0000real-space minimization; \u0000reciprocal-space minimization; \u0000simulated annealing; \u0000side-chain placement","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"152 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":"133957486","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}
引用次数: 38
X‐ray diffraction imaging of whole cells 全细胞的X射线衍射成像
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000826
D. Shapiro
{"title":"X‐ray diffraction imaging of whole cells","authors":"D. Shapiro","doi":"10.1107/97809553602060000826","DOIUrl":"https://doi.org/10.1107/97809553602060000826","url":null,"abstract":"","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"35 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":"121458248","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}
引用次数: 0
Chapter 20.2 Molecular-dynamics simulations of biological macromolecules 第20.2章生物大分子的分子动力学模拟
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000878
C. Post, V. M. Dadarlat
{"title":"Chapter 20.2 Molecular-dynamics simulations of biological macromolecules","authors":"C. Post, V. M. Dadarlat","doi":"10.1107/97809553602060000878","DOIUrl":"https://doi.org/10.1107/97809553602060000878","url":null,"abstract":"Advances in the theory of atomic interactions and the increasing availability of high-power computers have led to rapid development of the molecular-dynamics field and greater understanding of macromolecular motions. It is now practical to use molecular dynamics, in combination with crystallographic and NMR data, to search the large conformational space of proteins and nucleic acids to find structures consistent with the data and to improve the agreement with the data. The topics covered in this chapter include: the simulation method; potential-energy functions; empirical parameterization of the force field; modifications in the force field for structure determination; internal dynamics and average structures; assessment of the simulation procedure; and effect of crystallographic atomic resolution on structural stability during molecular-dynamics simulation. \u0000 \u0000 \u0000Keywords: \u0000 \u0000force fields; \u0000molecular dynamics; \u0000particle-mesh Ewald method; \u0000potential-energy functions; \u0000restraints","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"8 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":"122573788","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}
引用次数: 0
Ab initio phasing of low‐resolution Fourier syntheses 低分辨率傅立叶合成的从头算相位
International Tables for Crystallography Pub Date : 2012-04-14 DOI: 10.1107/97809553602060000852
V. Lunin, A. Urzhumtsev, A. Podjarny
{"title":"Ab initio phasing of low‐resolution Fourier syntheses","authors":"V. Lunin, A. Urzhumtsev, A. Podjarny","doi":"10.1107/97809553602060000852","DOIUrl":"https://doi.org/10.1107/97809553602060000852","url":null,"abstract":"Low-resolution phasing addresses the cases where experimental X-ray diffraction intensities are only available to a low-resolution limit, or when the standard phasing methods to solve macromolecular structures fail. Ab initio phasing is based on general properties of macromolecular objects (connectivity, electron-density histograms, likelihood of molecular masks etc.) and does not require extra diffraction experiments. The Monte Carlo phasing procedure includes generation of a large ‘population’ of trial solutions, enrichment of this population by filtering with selection criteria, clustering and averaging. The results of low-resolution phasing allow one to get information on the packing of particles in a crystal and on the shape (envelope) of the molecules, and to get an insight into the architecture of multidomain complexes. \u0000 \u0000 \u0000Keywords: \u0000 \u0000low-resolution phasing; \u0000ab initio phasing; \u0000low-resolution images; \u0000multifiltering cyclic phasing procedure; \u0000map connectivity; \u0000few-atoms model; \u0000phase averaging; \u0000Fourier synthesis; \u0000cluster analysis","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"35 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":"122683969","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}
引用次数: 3
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