Your self rotation strongly suggests a different spacegroup - I would look back at the integration and processing before puzzling over cell volumes! Eleanor
On Mon, 5 Jul 2021 at 16:00, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > 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 > 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> > *Sent:* Monday, July 5, 2021 10:25 AM > *To:* Robert S Phillips <p...@uga.edu>; CCP4BB@JISCMAIL.AC.UK < > 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> *Im Auftrag von *Robert > S Phillips > *Gesendet:* Montag, 5. Juli 2021 15:54 > *An:* 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 > 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 > ######################################################################## 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/
