Re: [ccp4bb] Unidentified electron density blob

[Wim Burmeister]

Hello, a really molecule should show up also in the 2Fo-Fc type map. This appears not to be the case. So indeed it is likely that your density corresponds to some alternate conformation of the surrounding residues present with low occupancy. The glutamic acid sidechain could be modelled, but I have some doubts about the rest. If the refinement is almost finished, it could simply be noise. Best Wim On 03/07/2018 04:23, Uma Gabale wrote: Dear all, We came across a blob of unidentified electron density in a shallow cavity of a bacterial protein structure (pictures attached). It is surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp. The protein was expressed in E. coli BL21(DE3) and purified on Ni-NTA followed by gel filtration. The purification buffers included Tris, crystallization condition had HEPES and PEG3350; perfluoropolyether was used as a cryoprotectant. We would appreciate any help in identifying it.​ Thanks and regards, Uma. -- Uma Gabale, PhD Research Associate Molecular and Cellular Biochemistry Indiana University Bloomington To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Wim Burmeister Professeur Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs CS 20192 38044 Grenoble Cedex 9, FRANCE E-mail: wim.burmeis...@ibs.fr Tel:    +33 (0) 457 42 87 41       Fax: +33 (0) 476 20 94 00 website map To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1