Hi Jakob, If there is radiation damage, for every "new" positive density there should be a negative density in the original position. From the pictures we've seen, it seems unlikely. Best, Nukri
On Wed, Jul 10, 2019 at 10:21 AM Keller, Jacob <[email protected]> wrote: > How about radiation-damaged/smashed Sulphur? You could test this by > refining occupancy of the cys S. > > > > JPK > > > > +++++++++++++++++++++++++++++++++++++++++++++++++ > > Jacob Pearson Keller > > Research Scientist / Looger Lab > > HHMI Janelia Research Campus > > 19700 Helix Dr, Ashburn, VA 20147 > > Desk: (571)209-4000 x3159 > > Cell: (301)592-7004 > > +++++++++++++++++++++++++++++++++++++++++++++++++ > > > > The content of this email is confidential and intended for the recipient > specified in message only. It is strictly forbidden to share any part of > this message with any third party, without a written consent of the sender. > If you received this message by mistake, please reply to this message and > follow with its deletion, so that we can ensure such a mistake does not > occur in the future. > > > > *From:* CCP4 bulletin board <[email protected]> * On Behalf Of *Lumbini > Yadav > *Sent:* Wednesday, July 10, 2019 7:12 AM > *To:* [email protected] > *Subject:* Re: [ccp4bb] Fo-Fc density close to cysteine residue > > > > Thank you for the valuable input > > > > On Wed, Jul 10, 2019 at 4:25 PM Eleanor Dodson <[email protected]> > 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 <[email protected]> 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 <[email protected]> > wrote: > > The key word for refmac is ANOM MAPONLY > > Are you using GUI2? > > Eleanor > > > > On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav <[email protected]> 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 <[email protected]> > 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:[email protected]] *On Behalf Of > *Lumbini > Yadav > *Sent:* Tuesday, July 09, 2019 5:22 AM > *To:* [email protected] > *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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=LU6cRtx0xgB8s29tIz9Olw&r=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI&m=Z963G6bopP8xJVXD1Wuy672eSOZyBi1ySdwyyfyUY28&s=eacDldZlgDNyZ5rJs_4-dTAl4HGX6sPpzGppOB85YNk&e=> > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=LU6cRtx0xgB8s29tIz9Olw&r=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI&m=Z963G6bopP8xJVXD1Wuy672eSOZyBi1ySdwyyfyUY28&s=eacDldZlgDNyZ5rJs_4-dTAl4HGX6sPpzGppOB85YNk&e=> > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=LU6cRtx0xgB8s29tIz9Olw&r=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI&m=Z963G6bopP8xJVXD1Wuy672eSOZyBi1ySdwyyfyUY28&s=eacDldZlgDNyZ5rJs_4-dTAl4HGX6sPpzGppOB85YNk&e=> > > ------------------------------ > > 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
