No I am using ccp4i. I tried doing SAD refinement in refmac and the output image is attached below . I do not seen density near cysteine that was visible in Fo-Fc map
On Wed, Jul 10, 2019 at 3:40 PM Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > The key word for refmac is ANOM MAPONLY > Are you using GUI2? > Eleanor > > On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav <lumbin...@gmail.com> wrote: > >> I have soaked my crystals in sodium dithionite a reducing agent. I have >> not done mass spec but sequence is confirmed >> >> On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel <dbon...@som.umaryland.edu> >> wrote: >> >>> Have you mass-speced the protein before crystallization to make sure it >>> wasn’t derivatized during expression and/or purification, or compared the >>> mass spec of the crystals verses purified protein? Any fancy reagents or >>> other reductants used during purification? >>> >>> What about S-Acetyl-cysteine (3-letter code: SCY). >>> >>> >>> >>> Best, >>> >>> >>> >>> Dan >>> >>> >>> >>> Daniel A Bonsor PhD. >>> >>> Sundberg Lab >>> >>> Institute of Human Virology >>> >>> University of Maryland, Baltimore >>> >>> 725 W Lombard Street N370 >>> >>> Baltimore >>> >>> Maryland >>> >>> MD 21201 >>> >>> Tel: (410) 706-7457 >>> >>> >>> >>> >>> >>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf >>> Of *Lumbini Yadav >>> *Sent:* Tuesday, July 09, 2019 5:22 AM >>> *To:* CCP4BB@JISCMAIL.AC.UK >>> *Subject:* [ccp4bb] Fo-Fc density close to cysteine residue >>> >>> >>> >>> Dear all, >>> >>> >>> >>> We have found a huge Fo-Fc density close to cysteine residue (see >>> attached image) in the structure with resolution of 1.2A. In the >>> crystallization condition, we have PEG 3350, Potassium phosphate >>> monobasic, glycerol and protein was in Tris and NaCl. Before freezing >>> the crystals were soaked in mother liquor containing sodium dithionite. >>> >>> >>> >>> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD, >>> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in >>> all the screenings we do see some part of Fo-Fc density unaddressed at >>> 3 sigma. >>> >>> >>> >>> Does anyone have an idea about what this density could be? Covalent >>> modification? >>> >>> >>> >>> Thanks. >>> >>> >>> >>> >>> >>> Kind regards, >>> >>> Lumbini >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
