Dear Mahmoud, The first thing to do is to make a list of (a) all your protein buffer components, (b) all your crystallisation conditions components, and (c) all the cryo-protection chemicals, and try to consider all of those as possibilities, but then again indeed it is most likely glycerol anyway ;-)
A, On 12 Sep 2023, at 14:48, Maria Håkansson <maria.hakans...@saromics.com<mailto:maria.hakans...@saromics.com>> wrote: Hi Mahmoud, It looks like glycerol (residue GOL in Coot) to me. Add it under File/Get Monomer GOL. There should be hydrogen bonds, at least one for it to turn up as well-ordered as below. Good Luck! Best regards, Maria From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Mahmoud RIZK <mahmoud.r...@esrf.fr<mailto:mahmoud.r...@esrf.fr>> Date: Tuesday, 12 September 2023 at 14:40 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] Unknown density in Trypsin Hi everyone, I am encountering a strong clear density within a structure of trypsin at 1.3 Å, please find attached a 360 rotation video of it, alternatively I uploaded it on YouTube: https://youtube.com/shorts/tHovB55lpio?feature=share the map shown here is a difference map at 3 sigmas. here is the its site with respect to the protein (image below): <fxQ0Bm9s9m758Vlz.png> (PS: this blob has been detected within different trypsin structures from several collected data.) (I tried checkmyblob.bioreproducibility.org<http://checkmyblob.bioreproducibility.org> without any success) I would greatly appreciate any suggestions on how to identify and characterize this blob. Thank you in advance for your assistance! With best regards, Mahmoud ________________________________ 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 ######################################################################## 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/
