Dear Thomas, Interestingly, I had crystallized the same protein with another ligand before with the same condition except that it had sodium citrate in addition. I was able to collect the data for this and it was a protein-ligand complex, which could be seen in the density. So I was speculating about this data especially because of the closely spaced diffraction spots, and if the crystal has some peculiar defect.
Thank you Regards Kavya On 2023-02-03 14:27, Thomas Flower wrote: > Dear Kavya, > > 4 mM is quite a high concentration of TCEP, perhaps they are TCEP crystals. > > You could try a Unit Cell Search of the CCDC to see if you find a match: Unit > Cell Search - WebCSD (cam.ac.uk) [2] > > Best, > > Thomas > > Thomas Flower, PhD > Senior Scientist, Protein Science > > Galapagos > 102 Avenue Gaston Roussel > 93230 Romainville > France > T: +33 7 81 26 95 70 > www.glpg.com [3] > > FROM: CCP4 bulletin board <[email protected]> ON BEHALF OF mesters@biochem > SENT: vendredi 3 février 2023 9:53 AM > TO: [email protected] > SUBJECT: Re: [ccp4bb] Regarding the diffraction image > > You don't often get email from [email protected]. Learn why this > is important [4] > > A and B unit cell dimensions are hardly bigger than twice the uni cell of > cubic NaCl and will probably not accommodate a 30 kDa protein. > > Make a SDS gel of washed & dissolved crystals to be sure these are not alt or > inhibitor crystals. You can stain the crystals with IzIt... > > J. > > -- > Dr. math. et dis. nat. Jeroen R. Mesters > https://orcid.org/0000-0001-8532-6699 [5] > > University of Lübeck > Institute of Biochemistry > https://www.biochem.uni-luebeck.de [6] > phone: +49-451-3101-3105 > Ratzeburger Allee 160 > 23562 Lübeck > Germany > -- > >> Am 03.02.2023 um 09:22 schrieb kavyashreem <[email protected]>: >> >> Dear all, >> >> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the >> condition 10%PEG3350, 50mM Zinc acetate. >> >> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8. >> >> >> Crystal: Crystal: >> crystal under UV m >> >> <b06fc576.png> <e091c7fd.png> <8ef9453e.png> >> >> When we collected the data at an in-house facility, it looked something like >> this: >> >> <b903961d.png> >> >> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. >> >> I have not come across a protein diffraction like this, nor of a salt. When >> I ran the gel for the incubated protein (protein+ligand), there was no >> degradation. >> >> Although, I was sure there is some problem with this image I tried >> processing, which could not be, But indexing showed a unit cell of 11Ang, >> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not the >> third. >> >> Can anyone please shed some light on this diffraction image? >> >> How can it happen? >> >> Thank you >> >> Regards >> >> Kavya >> >> ------------------------- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [1] > > ------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [1] This > e-mail and its attachment(s) (if any) may contain confidential and/or > proprietary information and is intended for its addressee(s) only. Any > unauthorized use of the information contained herein (including, but not > limited to, alteration, reproduction, communication, distribution or any > other form of dissemination) is strictly prohibited. If you are not the > intended addressee, please notify the originator promptly and delete this > e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any > of its affiliates shall be liable for direct, special, indirect or > consequential damages arising from alteration of the contents of this message > (by a third party) or as a result of a virus being passed on. > > ------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Links: ------ [1] https://eur05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7CThomas.flower%40GLPG.COM%7C44212ddb46284392893a08db05c40c61%7C627f3c33bccc48bba033c0a6521f7642%7C1%7C0%7C638110111905660899%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x6mbkUuRwfHe3zF3dDFIxgCOJU7uslR2iy%2FcVrLKWrY%3D&reserved=0 [2] https://www.ccdc.cam.ac.uk/structures/WebCSD/UnitCell [3] http://www.glpg.com/ [4] https://aka.ms/LearnAboutSenderIdentification [5] https://eur05.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0001-8532-6699&data=05%7C01%7CThomas.flower%40GLPG.COM%7C44212ddb46284392893a08db05c40c61%7C627f3c33bccc48bba033c0a6521f7642%7C1%7C0%7C638110111905504664%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BCI5EW%2B3Ha6ZJkPsy1sOX2ePH1Sa21Nm5iXg7%2F%2B64ys%3D&reserved=0 [6] https://eur05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biochem.uni-luebeck.de%2F&data=05%7C01%7CThomas.flower%40GLPG.COM%7C44212ddb46284392893a08db05c40c61%7C627f3c33bccc48bba033c0a6521f7642%7C1%7C0%7C638110111905660899%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=W%2FqGhyhxj72dqaDanauqUn0AwROzS5M4hH3xqrz6vXY%3D&reserved=0 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
