Re: [ccp4bb] electron density assignment
Generate an anomalous map and look for peaks. Many metals would generate anomalous. On 02/04/13 07:39, Gang Dong wrote: Dear all, Here are some hexmeric densities we observed in our 1.6-A resolution 2Fo-Fc map. They are located in between two dimers. Although 7 waters would fit nicely in the densities, we are not sure whether they might be something else (metals?). Any suggestions are welcome. Thanks! Gang ... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] electron density assignment
Hi, I observed a very similar hexagonal arrangement of electron density blobs in one of my structures recentely and asked the CCP4bb community to help me explain it. Unfortunately, noone could come up with some satisfactory explanation, so I gave up on interpreting this rogue density. What was certain beyond doubt is that it was somehow caused by the presence of cobalt ions. Do you, by chance, also have cobalt or similar ions present in your crystallization condition? Regards, Joern ** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ** On Mon, 4 Feb 2013, Gang Dong wrote: Dear all, Here are some “hexmeric” densities we observed in our 1.6-A resolution 2Fo-Fc map. They are located in between two dimers. Although 7 waters would fit nicely in the densities, we are not sure whether they might be something else (metals?). Any suggestions are welcome. Thanks! Gang [IMAGE] __ Gang Dong, PhD Junior Group Leader Max F. Perutz Laboratories (MFPL) Dr. Bohrgasse 9/3 A-1030 Vienna, Austria Phone: +43-1-4277-61625 FAX: +43-1-4277-9616 http://www.mfpl.ac.at/mfpl-group/group/dong.html Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] electron density assignment
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Gang, By chance, P222 is your space group? It seems to be three perpendicular two-fold axes are passing through your central atom which makes them all fall in the same plane. From the density it looks more like a water in the center but anomalous density map should help. Good luck. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Gang Dong gang.d...@univie.ac.at To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, 4 Feb 2013 13:39:39 +0100 Subject: [ccp4bb] electron density assignment *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear all, Here are some hexmeric densities we observed in our 1.6-A resolution 2Fo-Fc map. They are located in between two dimers. Although 7 waters would fit nicely in the densities, we are not sure whether they might be something else (metals?). Any suggestions are welcome. Thanks! Gang __ Gang Dong, PhD Junior Group Leader Max F. Perutz Laboratories (MFPL) Dr. Bohrgasse 9/3 A-1030 Vienna, Austria Phone: +43-1-4277-61625 FAX: +43-1-4277-9616 http://www.mfpl.ac.at/mfpl-group/group/dong.html --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
