Re: [ccp4bb] Unusual electron density - any guesses??
Well I would start by flipping the carbonyl oxygen then see if the side chain can use the density - what are the B values for the neighbouring stuff? Eleanor On 25 October 2013 19:00, Patel, Joe joe.pa...@astrazeneca.com wrote: Is that a glycine in the sequence next to the Glu/Gln? Have you tried building a 50% occ of the backbone in that region in two conformations, and then a water molecule further up into the feature. The density over the carbonyl looks weak and you have some negative density there that might indicate mixed conformation. Just an idea, hard to tell from still images if my idea would work. Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jose Artur Brito Sent: Friday, October 25, 2013 1:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusual electron density - any guesses?? Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
[ccp4bb] Unusual electron density - any guesses??
Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
Re: [ccp4bb] Unusual electron density - any guesses??
Is that a glycine in the sequence next to the Glu/Gln? Have you tried building a 50% occ of the backbone in that region in two conformations, and then a water molecule further up into the feature. The density over the carbonyl looks weak and you have some negative density there that might indicate mixed conformation. Just an idea, hard to tell from still images if my idea would work. Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jose Artur Brito Sent: Friday, October 25, 2013 1:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusual electron density - any guesses?? Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
