Absolutely agree Eleanor On 11 July 2017 at 22:06, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
> Still seems to me that the resolution could and should be pushed a little > further at least—CC1/2 is still high, completeness is good, I/sigma also is > good. Why not extend a little further, say to where one of these values > gets too low? Might improve the maps a bit. > > > > JPK > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Koromyslova, > Anna > *Sent:* Tuesday, July 11, 2017 3:37 PM > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* Re: [ccp4bb] Problem with a cell content > > > > Sorry for the confusion, NCS was found only in a dataset where the cell > dimensions were twice bigger regardless of the sp, and with a dimer as a > solution. The solvent content was the same. > > Peak Distance Vector > > 73.3% 143.8Å: FRAC +0.000 +0.000 -0.500 (ORTH -0.0 0.0 -143.8). > > There was no NCS in a dataset with a smaller unit cell and sp P6222. > > Thank you! > > > > Best regards, > > > > Anna > > > > > > > > Dr. Anna Koromyslova, Postdoctoral researcher > > German Cancer Research Center (DKFZ), F150 > > Im Neuenheimer Feld 242 > > D-69120 Heidelberg > > Germany > > > > > > *From: *Eleanor Dodson <eleanor.dod...@york.ac.uk> > *Date: *Tuesday, July 11, 2017 at 8:17 PM > *To: *"Koromyslova, Anna" <a.koromysl...@dkfz-heidelberg.de> > *Cc: *"CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk> > *Subject: *Re: [ccp4bb] Problem with a cell content > > > > So SG could be P31 2 2 > > What is the height of NCS vector v origin? > > Eleanor > > Look at hklview to see hk i sections. Obviously all l = odd will be weak. > > > > > > On 11 July 2017 at 19:12, Koromyslova, Anna <a.koromyslova@dkfz- > heidelberg.de> wrote: > > Dear Eleanor, > > > > NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or > C121. All had the same solution. > > The protein tends to form a homodimer and if I use P1 space group > molecular replacement can find several dimers, there is no translational > ncs found during MR, but still solvent cell content was similarly high. > > Within a protein monomer there are no similar domains. > > > > Best regards, > > Anna > > > > > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor > Dodson <eleanor.dod...@york.ac.uk> > *Reply-To: *Eleanor Dodson <eleanor.dod...@york.ac.uk> > *Date: *Tuesday, July 11, 2017 at 7:29 PM > *To: *"CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> > *Subject: *Re: [ccp4bb] Problem with a cell content > > > > This is very strange . If you have a large non- crystallographic > translation vector you would expect either to have two molecules in the > asymmetric unit or your one molecule must have two very similar domains? > > What is the n-c translation vector? > > > > Could you have assigned too high symmetry ? SG maybe P 62? That could > explain the packing clashes Z scores of 27 are pretty good. > > > > Eleanor > > > > > > On 11 July 2017 at 18:05, Oganesyan, Vaheh <oganesy...@medimmune.com> > wrote: > > Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших > кристаллов? Кристаллы бывают разные. > > > > First of all Fab by itself is already almost 50 kDa, so complex with > antigen should be more than 50 kDa. Because you already solved the > structure calculate the molecular mass based on your pdb file and rerun > Matthews with correct mass. New numbers may be quite a bit different. Good > indication of relatively low crystal density and consequently loose packing > is the resolution of your data set. If you did not throw away data beyond > 2.9A I’d suggest use them all. The reflections are too valuable to throw > away. If data beyond some resolution is weak then they will have low > contribution to the structure. Best if you calculate electron density maps > at different resolutions at the end of refinement, compare them and use > resolution that makes difference. > > > > > > > > *Regards,* > > > > *Vaheh* > > *8-5851* > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Koromyslova, > Anna > *Sent:* Tuesday, July 11, 2017 12:32 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Problem with a cell content > > > > Dear CCP4 members, > > > > I am working on a structure of a protein in complex with an antibody > fragment (approx. 50kDa together). Molecular replacement with closely > related proteins always comes up with one complex in the asymmetric unit, > although MW of protein to which Matthews applies is 125kDa and corresponds > to two complexes. > > Phaser gives two warnings: > > Large non-origin Patterson peak indicates that translational NCS is > present. > > Solutions with Z-scores greater than 27.2 (the threshold indicating a > definite solution) were rejected for failing packing test > > > > I couldn’t get a solution with two subunits although I have tried multiple > combinations including only conserved parts of both proteins and different > space groups including P1. Phenix Autobuild also yielded only one complex. > > > > So, the question is whether I can use that structure as is despite very > high solvent content (80%) or should I try smth else. I would be very > grateful for any suggestions. > > > > When the solution with a single complex is refined the statistics are the > following: > > > > R-work 0.2129 > > R-free 0.2459 > > Matthews Coefficient: 6.22 > > Percentage Solvent: 80.22 > > Resolution range (Å) 48.34 - 2.9 (2.98 - 2.9) > > Space group P 62 2 2 > > Unit cell 167.45 167.45 143.538 90 90 120 > > Multiplicity 19.1 (18.3) > > Completeness (%) 99.44 (94.39) > > Mean I/sigma(I) 24.59 (2.71) > > Wilson B-factor 64.28 > > R-merge 0.1256 (1.186) > > R-meas 0.1291 > > CC1/2 0.999 (0.85) > > CC* 1 (0.959) > > > > Thank you very much for your help, > > > > Anna > > > > > > Dr. Anna Koromyslova, Postdoctoral researcher > > German Cancer Research Center (DKFZ), F150 > > Im Neuenheimer Feld 242 > > D-69120 Heidelberg > > Germany > > > > To the extent this electronic communication or any of its attachments > contain information that is not in the public domain, such information is > considered by MedImmune to be confidential and proprietary. This > communication is expected to be read and/or used only by the individual(s) > for whom it is intended. If you have received this electronic communication > in error, please reply to the sender advising of the error in transmission > and delete the original message and any accompanying documents from your > system immediately, without copying, reviewing or otherwise using them for > any purpose. Thank you for your cooperation. > > > > >
