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Well - that more or less proves the residue is a CYS - there is a peak in the PHAN map right on the S. And that the extra density does not contain an anomalous scatterer so is probably not a metal or a sulphate or... But that still doesnt explain WHAT it is . Sorry not to be more help.. Eleanor On Wed, 10 Jul 2019 at 11:32, Lumbini Yadav <[log in to unmask]> wrote: > 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 <[log in to unmask]> > wrote: > >> The key word for refmac is ANOM MAPONLY >> Are you using GUI2? >> Eleanor >> >> On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav <[log in to unmask]> 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 <[log in to unmask]> >>> 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:[log in to unmask]] *On Behalf >>>> Of *Lumbini Yadav >>>> *Sent:* Tuesday, July 09, 2019 5:22 AM >>>> *To:* [log in to unmask] >>>> *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