I am serious about checking the anomalous map!! (trivial from REFMAC - key word anom map on) Then do a peak search and just check first that the rogue residue IS CYS first - you should see the S as a peak..)
Eleanor On Wed, 10 Jul 2019 at 07:38, Lumbini Yadav <[email protected]> wrote: > Thanks for the reply. > The distance between sulphur and centre of Fo-Fc map is around 2.5A. The > density does not appear to be of hydrogen (attached image) anisotropy > refinement also does not help. > > On Tue, Jul 9, 2019 at 5:13 PM Anthony Addlagatta <[email protected]> > wrote: > >> Lumbini, >> >> It would useful to know the distance between the sulfur and center of the >> Fo-Fc map that you have shown. Since you have very high resolution data, >> the extra density could be for a hydrogen atom in CSO-H (sufeneic acid) or >> anisotropy of the oxygen atom. >> >> Anthony >> ------------------------------ >> *From: *[email protected] >> *To: *[email protected] >> *Sent: *Tuesday, July 9, 2019 4:48:32 PM >> *Subject: *Re: [ccp4bb] Fo-Fc density close to cysteine residue >> >> Any anomalous diffraction? >> >> On Tue, 9 Jul 2019 at 10:32, Lumbini Yadav <[email protected]> wrote: >> >>> 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 >> > > ------------------------------ > > 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
