Re: [ccp4bb] Request for assistance with structure solution
Thank you @Yehudi BLOCH, Kay for the help. Kind Regards, Adewumi Adeyeye, (PhD Candidate)Department of Biochemistry, Genetics, and Microbiology Structural Biology Group, Room 3-7, Agricultural Sciences Building, University of Pretoria c/o University & Lynnwood Roads Hatfield Pretoria 0083 Cell: +27638643131 South Africa On Wednesday, April 17, 2024 at 10:48:04 AM GMT+1, Kay Diederichs wrote: good detective work indeed! Kay On Tue, 16 Apr 2024 14:40:15 +0100, Yehudi BLOCH wrote: >Dear Adewumi > >I'm afraid the 85% complete dataset is a contaminant as well. >PDB 2r6s and related entries for E.coli Gab protein have near identical unit >cell parameters. The autoprocessed (?) .mtz file you attached also solves with >this E.coli protein. >I suppose that if you rerun XDS with the given unit cell parameters things >should process. > >Best >Yehudi > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Request for assistance with structure solution
good detective work indeed! Kay On Tue, 16 Apr 2024 14:40:15 +0100, Yehudi BLOCH wrote: >Dear Adewumi > >I'm afraid the 85% complete dataset is a contaminant as well. >PDB 2r6s and related entries for E.coli Gab protein have near identical unit >cell parameters. The autoprocessed (?) .mtz file you attached also solves with >this E.coli protein. >I suppose that if you rerun XDS with the given unit cell parameters things >should process. > >Best >Yehudi > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Request for assistance with structure solution
Dear Adewumi I'm afraid the 85% complete dataset is a contaminant as well. PDB 2r6s and related entries for E.coli Gab protein have near identical unit cell parameters. The autoprocessed (?) .mtz file you attached also solves with this E.coli protein. I suppose that if you rerun XDS with the given unit cell parameters things should process. Best Yehudi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Request for assistance with structure solution
Good morning Adewumi Adeyeye, I'll look at the problem but I need the raw data. Please upload the *.h5 files from this crystal to some cloud service, and send me the link. Best wishes, Kay Am 12.04.24 um 10:40 schrieb Adewumi Adeyeye: Good day, I am writing to seek your help with resolving the problems I have been having solving the structure of my protein. I collected my data on the Beamline I04 of the Diamond Light Source. There were at least 4 different types of crystals in the collection. Unfortunately, I couldn't get a solution. However, with the assistance of yourself and other experts, we identified that my best data belong to a contaminant protein. Afterwards, I decided to inspect all the other dataset. I noticed there is a dataset which reported 85% completeness. Upon analysis with Xtriage it suggested indexing at a lower space group. I suspect this dataset might belong to my protein of interest. The images show that it is my crystal of interest that was loaded giving this dataset. I would really love to explore this. I have downloaded the dataset and tried using XDS to index but my results have been inconsistent. Initially, the process was smooth all the way through and yielded hkl file. Subsequent attempt failed to even proceed beyond IDXREF. I don't know what I am doing wrong. Any help would be so much appreciated Thank you. Inline image Inline image Kind Regards, Adewumi Adeyeye, (PhD Candidate) Department of Biochemistry, Genetics, and Microbiology Structural Biology Group, Room 3-7, Agricultural Sciences Building, University of Pretoria c/o University & Lynnwood Roads Hatfield Pretoria 0083 Cell: +27638643131 South Africa -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s". To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ smime.p7s Description: Kryptografische S/MIME-Signatur
