Rob, Wat is the Matthews number, would it fit with a very low percentage solvent, or would it not fit at all? What happens if you superimpose a tetramer on your dimer?
Best, Herman Von: Robert S Phillips <p...@uga.edu> Gesendet: Montag, 5. Juli 2021 16:32 An: Schreuder, Herman /DE <herman.schreu...@sanofi.com> Betreff: Re: Strange indexing problem Herman: That is the problem. The unit cell in P1 will only accept a dimer, and the real asymmetric unit must be a tetramer. I tried to double the dimension of the unit cell and reintegrate. That gave acceptable statistics, but molecular replacement gave two separate dimers, not a tetramer, and it still did not refine. Rob Robert S. Phillips Professor of Chemistry and of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602 Phone: (706) 542-1996 Fax: (706) 542-9454 E-mail: rsphill...@chem.uga.edu<mailto:rsphill...@chem.uga.edu> Web: http://tryptophan.net<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpod51004.outlook.com%2Fowa%2Fredir.aspx%3FC%3Dccbf42ffea5f48b1bf8e9bb950454bab%26URL%3Dhttp%253a%252f%252ftryptophan.net&data=04%7C01%7CHerman.Schreuder%40sanofi.com%7C480e122de54943e9cc0108d93fc1ac73%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637610923344729892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=aaZEYjjaLJctM7%2FpKbqBlute4JRdIfpQnXxl8MxTWyM%3D&reserved=0> ________________________________ From: Schreuder, Herman /DE <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> Sent: Monday, July 5, 2021 10:25 AM To: Robert S Phillips <p...@uga.edu<mailto:p...@uga.edu>>; CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: AW: Strange indexing problem [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Dear Rob, Your screen shot shows a large empty region with difference density for the second half of the tetramer, so the my guess is that you have a tetramer in the asymmetric unit, but that your molrep program only found a dimer. Would a tetramer fit in the asymmetric unit? If you have a tetramer in the asymmetric unit, there are several things you could do: 1. Construct a tetramer and use that as a search model. 2. Truncate surface loops, which may lead to rejection of valid solutions due to clashes. 3. Set the maximum allowed number of clashes higher to prevent rejection. However, if only a dimer would fit in the asymmetric unit, you have a problem and you may want to search for statistical disorder in protein crystals. Good luck, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Robert S Phillips Gesendet: Montag, 5. Juli 2021 15:54 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [ccp4bb] Strange indexing problem I collected data last week on crystals of tyrosine phenol-lyase obtained under new conditions. The data have higher resolution than previous crystals, to 1.5 A. However, I can't get them to index in any space group but P1. Usually, the space group is P21212. The self-rotation function is attached. The P1 data will give a molecular replacement solution, but it does not refine below 0.46. The P1 asymmetric unit fits a dimer, but the assembly is a tetramer. In the map, I can see the difference peaks from the other dimer of the tetramer. What could be causing this problem? Rob Robert S. Phillips Professor of Chemistry and of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602 Phone: (706) 542-1996 Fax: (706) 542-9454 E-mail: rsphill...@chem.uga.edu<mailto:rsphill...@chem.uga.edu> Web: http://tryptophan.net<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpod51004.outlook.com%2Fowa%2Fredir.aspx%3FC%3Dccbf42ffea5f48b1bf8e9bb950454bab%26URL%3Dhttp%253a%252f%252ftryptophan.net&data=04%7C01%7CHerman.Schreuder%40sanofi.com%7C480e122de54943e9cc0108d93fc1ac73%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637610923344729892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=aaZEYjjaLJctM7%2FpKbqBlute4JRdIfpQnXxl8MxTWyM%3D&reserved=0> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CHerman.Schreuder%40sanofi.com%7C480e122de54943e9cc0108d93fc1ac73%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637610923344739852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xCLjdtMOG7HGkbh1L1xt1%2BgLJr0mQAcXrAUSThW9ASI%3D&reserved=0> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
