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. >
