Hi ???, I would first try AMPLE, as was suggested by Daniel.
If separate helices still give you an anti-parallel coiled coil, your structure may in fact be anti-parallel. Your problem is not that the structure has another parallelity than you would like, but that you cannot solve the MR problem. If your structure turns out to be anti-parallel, that’s what it is, as long as the structure has been solved correctly. How do your electron density maps look like: do you see any difference density for mutated side chains? Do you see any hints how to extend your shorter model? Did you do any refinement? If your MR solution is basically correct, the Rfactor might drop quite quickly during refinement, if not, the Rfactor may stay stuck or explode. Best, Herman Von: 张士军 [mailto:21620150150...@stu.xmu.edu.cn] Gesendet: Freitag, 21. Juli 2017 12:56 An: Schreuder, Herman /DE Betreff: Re: AW: [ccp4bb] high Rfree Hi The resolution of my data is 2.8A, and the Rfree/Rwork are 0.55/0.49 which are very high. And I was separate them when I do MR, the solution is still anti-parallel coiled-coil after MR. Does it mean I MUST DO anomolous phasing ? -----原始邮件----- 发件人:herman.schreu...@sanofi.com 发送时间:2017-07-21 15:37:33 (星期五) 收件人: 21620150150...@stu.xmu.edu.cn<mailto:21620150150...@stu.xmu.edu.cn>, CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 抄送: 主题: AW: [ccp4bb] high Rfree Hi ???, Coiled coil structures can be very tricky with MR, so your solution may not be correct. You could try to split your search model and run MR with the separate coils. If you have high enough resolution (> ~2.3 Å?) and your MR solution is basically correct, you may be able to solve your problem by rebuilding and refinement, but this may be a lot of work. Without any details (resolution of the data, current Rwork/Rfree etc.) it is difficult to give any more specific advice. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von ??? Gesendet: Freitag, 21. Juli 2017 03:17 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [ccp4bb] high Rfree Hi everyone I have got a anti-parallel coiled-coil structure in a short fragment recently, then I want to solve a longer fragment structure with phenix-MR using this short fragment structure as a model.The result is not good because of the Rwork and Rfree is high.So<https://urldefense.proofpoint.com/v2/url?u=http-3A__high.So&d=DQQGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=66oGBkFu_vOT7n3Fp-7licSV3JzUrtBbobSB9EEKws0&s=wYjH3MkMtX51bkladsLunNIv3g08mTlwh2zW9rna7rA&e=> I think the longer fragment will be parallel coiled-coil which is different with the shorter one. I am wondering whether there are any other methods to handle this phenomenon besides heavy atom phasing? Thanks a lot!!!
