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Thank you for the valuable input On Wed, Jul 10, 2019 at 4:25 PM Eleanor Dodson <[log in to unmask]> wrote: > 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