Oxygen additions in serial femtosecond crystallographic protein structures
In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation‐induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data s...
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| Veröffentlicht in: | Protein science 2016-10, Vol.25 (10), p.1797-1802 |
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| creator | Wang, Jimin |
| description | In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation‐induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R‐factors of the resulting structural model. |
| doi_str_mv | 10.1002/pro.2987 |
| format | Article |
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However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R‐factors of the resulting structural model.</description><identifier>ISSN: 0961-8368</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1002/pro.2987</identifier><identifier>PMID: 27438534</identifier><identifier>CODEN: PRCIEI</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Chemical reactions ; cryroprotectants ; Crystallography ; Crystallography, X-Ray ; Data collection ; dirty diffraction data ; dirty enzyme ; free radical amplifiers ; free radical chain reaction ; Models, Molecular ; Oxygen ; Oxygen - chemistry ; Proteins - chemistry ; radiation chemistry ; serial femtosecond crystallography ; SFX ; XFEL ; X‐ray free‐electron laser</subject><ispartof>Protein science, 2016-10, Vol.25 (10), p.1797-1802</ispartof><rights>2016 The Protein Society</rights><rights>2016 The Protein Society.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5047-7aa4f69fd68e47094fb7a9e614d922a831d40808bf9fde72e9785bcb9601de863</citedby><cites>FETCH-LOGICAL-c5047-7aa4f69fd68e47094fb7a9e614d922a831d40808bf9fde72e9785bcb9601de863</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029527/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029527/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,724,777,781,882,1412,1428,27905,27906,45555,45556,46390,46814,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27438534$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Jimin</creatorcontrib><title>Oxygen additions in serial femtosecond crystallographic protein structures</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation‐induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R‐factors of the resulting structural model.</description><subject>Chemical reactions</subject><subject>cryroprotectants</subject><subject>Crystallography</subject><subject>Crystallography, X-Ray</subject><subject>Data collection</subject><subject>dirty diffraction data</subject><subject>dirty enzyme</subject><subject>free radical amplifiers</subject><subject>free radical chain reaction</subject><subject>Models, Molecular</subject><subject>Oxygen</subject><subject>Oxygen - chemistry</subject><subject>Proteins - chemistry</subject><subject>radiation chemistry</subject><subject>serial femtosecond crystallography</subject><subject>SFX</subject><subject>XFEL</subject><subject>X‐ray free‐electron laser</subject><issn>0961-8368</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kU1LHEEQhhuJZNc14C8IA7l4Ge2v6Y-LEESNIqyECN6anp6a3ZbZ6bV7xmT_vTNx1RjwVBT18FQVL0IHBB8RjOnxOoYjqpXcQVPChc6VFnef0BRrQXLFhJqgvZTuMcacUPYZTajkTBWMT9HV_M9mAW1mq8p3PrQp822WIHrbZDWsupDAhbbKXNykzjZNWES7XnqXDSs7GNku9q7rI6R9tFvbJsGXbZ2h2_OzX6c_8uv5xeXp9-vcFZjLXFrLa6HrSijgEmtel9JqEIRXmlKrGKk4VliV9cCApKClKkpXaoFJBUqwGTp59q77cgWVg7aLtjHr6Fc2bkyw3ryftH5pFuHRFJjqgspBcLgVxPDQQ-rMyicHTWNbCH0yRFHKhWB6RL_9h96HPrbDeyNFBGOS0jehiyGlCPXrMQSbMaChD2YMaEC__nv8K_iSyADkz8Bv38DmQ5G5-Tn_K3wCveacAw</recordid><startdate>201610</startdate><enddate>201610</enddate><creator>Wang, Jimin</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7T5</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201610</creationdate><title>Oxygen additions in serial femtosecond crystallographic protein structures</title><author>Wang, Jimin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5047-7aa4f69fd68e47094fb7a9e614d922a831d40808bf9fde72e9785bcb9601de863</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Chemical reactions</topic><topic>cryroprotectants</topic><topic>Crystallography</topic><topic>Crystallography, X-Ray</topic><topic>Data collection</topic><topic>dirty diffraction data</topic><topic>dirty enzyme</topic><topic>free radical amplifiers</topic><topic>free radical chain reaction</topic><topic>Models, Molecular</topic><topic>Oxygen</topic><topic>Oxygen - chemistry</topic><topic>Proteins - chemistry</topic><topic>radiation chemistry</topic><topic>serial femtosecond crystallography</topic><topic>SFX</topic><topic>XFEL</topic><topic>X‐ray free‐electron laser</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Jimin</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Immunology Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Protein science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Jimin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Oxygen additions in serial femtosecond crystallographic protein structures</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>2016-10</date><risdate>2016</risdate><volume>25</volume><issue>10</issue><spage>1797</spage><epage>1802</epage><pages>1797-1802</pages><issn>0961-8368</issn><eissn>1469-896X</eissn><coden>PRCIEI</coden><abstract>In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation‐induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R‐factors of the resulting structural model.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>27438534</pmid><doi>10.1002/pro.2987</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Chemical reactions cryroprotectants Crystallography Crystallography, X-Ray Data collection dirty diffraction data dirty enzyme free radical amplifiers free radical chain reaction Models, Molecular Oxygen Oxygen - chemistry Proteins - chemistry radiation chemistry serial femtosecond crystallography SFX XFEL X‐ray free‐electron laser |
| title | Oxygen additions in serial femtosecond crystallographic protein structures |
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