Hi Eleanor,Thanks for asking. Yes, 2nd domain refine alright with Rfree ~25%, inhibitor at the binding site and no major issues at all except that I don't see any trace of 1st domain and the protein from dissolved crystals are on SDS gel at right MW size = 1st+2nd domain.I tried all other possible space group of P3. Only P31 works with ~26% Rfree but with 2 monomers of BD2. Strangely, I find this phenomenon only in presence of a specific inhibitor. Unliganded protein structure ~2A and with few other inhibitors (1.5-2.2A) all have two domains. Just can't wrap my head around the mystery. Thanks,Reza
Md Rezaul Karim PhD candidate PhD Program in Integrated Biomedical Sciences Dept. of Molecular Medicine, Morsani College of Medicine, USF,Tampa Schonbrunn lab, Moffitt Cancer Center, Tampa Email: rez...@health.usf.edu, md.ka...@moffitt.org Phone: (813) 745 4673 ext. 5462 On Mon, Sep 14, 2020 at 5:50 AM, Eleanor Dodson<eleanor.dod...@york.ac.uk> wrote: Rezaul: You sayBut I only see the 2nd domain with exact same unit cell that I have solved for 2nd domain's with same space group. I am afraid if that is so that you probably have only crystallised the 2nd domain. Does that domain refine all right?Eleanor On Mon, 14 Sep 2020 at 09:02, Rezaul Karim <00001e364c8f16de-dmarc-requ...@jiscmail.ac.uk> wrote: Eagerly following >I have a similar case. A 3A data with P3(1)21 from two domains (80+% sequence identity) protein. No major twinning issue. But I only see the 2nd domain with exact same unit cell that I have solved for 2nd domain's with same space group. No proteolysis- crystals give protein band on SDS at right MW. Data from 20+ crystals from various condition & additive screens came out all the same.Resorted to changing the construct to make variable N/C-term for future. Thanks,Reza Md Rezaul Karim Postdoctoral Research FellowH. Lee Moffitt Cancer Center and Research InstituteTampa, FL Email: rez...@health.usf.edu, reza.ka...@moffitt.org Phone: (813) 745 4673 ext. 5462 On Sun, Sep 13, 2020 at 7:33 PM, Jon Cooper<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: Hello, a couple of thoughts. If your best dataset has a twinning fraction of 40% (i.e. almost 50:50 ;-?) and the twin operator corresponds to a 2-fold rotation parallel to the z-axis, is it definitely trigonal, rather than hexagonal? The 2-fold NCS operator that you found for the d3 domains, is it parallel to an axis, e.g. z? Also, how long did the crystals take to grow and do you have the original diffraction images? If so, and I know its hard to tell with fine-slicing on modern detectors, do they look clean or do they show any splitting of the spots, etc? Also, a bit boring question, but when you say the space group is P32, I guess you mean P3 subscript(2) rather than P321, and I take it you have tried alternative space groups in the MR like P3 subscript(1). Are the systematic absences good, or is it all a bit ambiguous? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent with ProtonMail Secure Email. ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Tuesday, 8 September 2020 19:53, Andrew Lovering <a.lover...@bham.ac.uk> wrote: Dear all, I've a project with two historical datasets (i.e. not sure of when/if I can reproduce to solve problem by getting better data) that are twinned. The spacegroup is P32, with operator -h, -k, l cell = 83.5 83.5 64.2 90 90 120 protein has three domains d1-d2-d3, likely 50% solvent, 2 copies in asu dataset 1, roughly 3.6 angstrom resolution, twin fraction 0.25 dataset 2, roughly 3.1 angstrom resolution, twin fraction 0.4 I've managed to solve this (unambiguously) by finding a d3:d3 dimer in detwinned data, then seeing via phenix autobuild that it finds a d2 also in map. At present the ability to interpret the map further stalls there, and it can't be "the limit" because lack of crystal contacts suggest there should be more protein to find..... I realise I can go two ways, either using the detwinned data or using twinned data and supplying the operator.....the former giving ridiculously optimistic R-values with a suspiciously "clean map", the latter giving noisier but maybe more informative maps. Two-fold averaging is not going to be great because the d2-d3 arrangement observed in monomer 1 clashes when placed over monomer 2 (so at present can only average the small % of ASU between d3 copies). Critically, looking for a second d2 using MR fails but the lack of crystal contacts suggests success should be possible....its really unlikely that a third entity is in there (d1 and d2 are actually 50% similar, so by searching for d2 and failing, I'm actually missing three spots it could potentially occupy if the protein is not proteolysed) Sorry for long email but the devil is in the details. My question would be, what is best practice in a low res poor twinned dataset where you can only fill roughly just over half of what should be in there? Feel free to tell me its doomed! Best wishes & thanks in advance Andy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 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/
