Percent of identity/similarity is a number that might be often misleading when used as a judgement rule for molecular replacement. Very high or very low numbers are almost always indicative of corresponding outcome. The numbers in twilight zone of 20 to 35%, however, are not. When aligning sequences of target protein with potential MR models pay attention to residues like Cys, Trp, Phe, Tyr. Last three could be used in place of each other. Aligned Cys, for example, are very good indication of fold similarity. Ding between aligned Cys is indicative of difference in loop lengths, etc. When possible use more sequences to align, not just two. Also, there might be some info about your protein’s either binding partner or an active site, if it is an enzyme. In that case check out alignment of residues associated with the function.
Regards, Vaheh Oganesyan www.medimmune.com From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Nishant Varshney Sent: Tuesday, August 29, 2017 6:51 AM To: [email protected] Subject: [ccp4bb] NMR or Homology Model as a MR model Dear Crystallographers, I am working to solve an human protein structure which has a domain sequence identity of 24% with domain of another protein. As Phaser as well as Molrep failed to give any definite solution (TFZ=3.7 from MR), I want to ask, if solution structure of another protein having domain sequence similarity of 25% or a homology model can be used as a template for MR? Many thanks and Regards Nishant -- Dr. Nishant Kumar Varshney, Research Associate, C/O Dr. Sameena Khan, Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI) NCR Biotech Science Cluster, 3rd Milestone, Faridabad – Gurgaon Expressway, Faridabad – 121001 (HARYANA), India Ph: +91- 0129-2876477<tel:+91%20129%20287%206477> Mob: 8390564690 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
