Dear Chen, Is this an icosahedral virus crystal structure, or a highly symmetric structure where the RNA may have different binding modes to each subunit and thus averaged out in the crystal?
Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicolas FOOS [nicolas.f...@esrf.fr] Sent: Wednesday, June 21, 2017 4:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Weak density of RNA in a complex structure Dear Chen, I will answer with some question : - How is the refinement going ? Is the RNA properly taking in count ? Which soft do you use ? - How do you solve the structure ? MR ? If it's MR did you use a model which contain both protein and RNA ? Did you try to solve with the protein only ? Maybe you are "forging" RNA. - Depending of your data (wavelenght and redundancy) you can try to calculate an anomalous difference map to see the phosphorus of the RNA to be more confident. - Last point, it could be the occupancy connected with the stability of the complex, maybe sometimes RNA is here sometimes not. I see that one time with two complex in the same ASU, one has one missing partner. For my side, I really like to refine my DNA-protein complex with Buster from global Phasing. It gives you a very nice and informative density map. If you have this possibility let's try. Hope to help. Nicolas Nicolas Foos PhD Structural Biology Group European Synchrotron Radiation Facility (E.S.R.F) 71, avenue des Martyrs CS 40220 38043 GRENOBLE Cedex 9 +33 (0)6 76 88 14 87 +33 (0)4 76 88 45 19 On 21/06/2017 09:34, Chen WeiFei wrote: Dear All, We have get a complex crystal and the resolution can be refined to nearly 1.84 Å. But the electron density of the RNA is very weak. In some datasets we can't find any density of the RNA and in other datasets we can see more or less some RNA density. For now we can build 6-7 nucleotides but we can't distinguish the rigth sequence. If anyone has the same problem and how to solve this problem. Best Regards, Dr Wei-Fei Chen College of Life Sciences, Northwest A&F University
