Dear Gottfried Assuming your modelling is correct you can always try occupancy refinement of your ligand (or simply test alternative values). Maybe that will help. You can also play with bulk solvent mask parameters. Keywords (both occupancy and mask parameters) can be found in https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#id.b236767394ac
Best wishes Roberto Roberto A Steiner www.steinerlab.org<http://www.steinerlab.org/> https://twitter.com/steiner_lab roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk> Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.stei...@unipd.it<mailto:roberto.stei...@unipd.it> Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours. On 14 Dec 2023, at 11:20, Palm, Gottfried <0000b793af054fc6-dmarc-requ...@jiscmail.ac.uk<mailto:0000b793af054fc6-dmarc-requ...@jiscmail.ac.uk>> wrote: You don't often get email from 0000b793af054fc6-dmarc-requ...@jiscmail.ac.uk<mailto:0000b793af054fc6-dmarc-requ...@jiscmail.ac.uk>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear all, I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a main chain N, one of the ring nitrogens to a glutamate side chain. At occupancy 1.0 I get B-factors twice as high as the protein and negative difference density. Thus, I set the occupancy to 0.5 and get the whole EPE covered in positive difference density at 3 sig, peaking at 6 sig. This positive density is much larger than without EPE. On first glance, this looked contradictory to me: more positive density after putting more atoms there. I can only guess that the solvent at the place of the EPE is set to 0 (instead of 0.5), so I get positive density because of only 0.5 occupied EPE. Can I refine with half a ligand and half solvent? Greetings Gottfried On Tuesday, 12-12-2023 at 09:50 Krieger, James M wrote: There is also discussion about this for chaperonins such as CCT and GroEL. It may be that beryllium fluoride works better. Best wishes James > On 12 Dec 2023, at 05:30, Matthew BOWLER > <mbow...@embl.fr<mailto:mbow...@embl.fr>> wrote: > > Dear Jinyu, > we observed exactly this in PGK - see https://doi.org/10.1021/ja100974t where > we confirmed it by both crystallography and 19F NMR > > In fact ALF3 does not exist as a trigonal bipyramid - all cases where this > geometry is observed are likely MgF3 that does adopt this geometry and will > replace the aluminium at pH values above 8 as Al will precipitate as AlOH. > > We only saw the water replacing the F when a catalytic residue charge was > removed and proposed the hypothesis that phos transfer enzymes need to > balance the charge in the active site exactly therefore selecting the neutral > AlF3 over negative AlF4- that both exist in solution. > > Best wishes, Matt > >> On 2023-12-12 03:40, Friday wrote: >> Dear CCP4 community, >> I recently tried to use AlF3 to mimic the transition of an enzyme. In >> all the publications I can find, when mimicking the 3rd phosphate of >> the transition state, the AlF3 forms a trigonal bipyramid >> coordination, and the G(A)DP oxygen to the AL is about equal distance >> to that from the AL to the catalytic water oxygen (2.2A). >> However, I got a completely different geometry of ALF3, I think I have >> the ALF3OH bound and it's a tetrahedron geometry instead of trigonal >> pyramidal. The G(A)DP oxygen to the AL is about 3.1A and the AL to >> the catalytic water oxygen is about 1.8A. >> I am pretty sure it is not the ALF4 but the ALF3OH since the AL-OH >> distance is longer than the Al-F distance (1.8A verse 1.6A) and I have >> a very high resolution structure. >> Can anyone explain this to me, have you ever encountered this before? >> Your answer is much appreciated! >> Jinyu >> ------------------------- >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > Matthew Bowler > Project Leader MASSIF1@ESRF > European Molecular Biology Laboratory > 71 avenue des Martyrs > CS 90181 F-38042 Grenoble > France > =================================================== > Tel: +33 (0) 4.76.20.76.37 > Fax: +33 (0) 4.76.20.71.99 > > http://www.embl.fr<http://www.embl.fr/>/ > http://www.esrf.eu/MASSIF1 > https://twitter.com/id30_massif1 > https://www.embl.org/people/person/mbowler/ > =================================================== > > ######################################################################## > > 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 http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by > http://www.jiscmail.ac.uk<http://www.jiscmail.ac.uk/>/, terms & conditions > are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk/>, terms & conditions are available athttps://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ 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/
