Hmmm - something is wrong here. The two sets of cell dimensions are closely relatable a1=a2. C2=2b1. C1=b2 but The beta angle 98 for the I2 space group is inconsistent.. can you see the predicted spots on an image?
Re the translation peak (0.5,0,0) dies your model have any pseudo symmetry? Eleanor And for the C2 2 21 data I guess you tried all space groups in the pointgroup? On Thu, 17 Apr 2025 at 05:37, Rezaul Karim < [email protected]> wrote: > Since the Xtriage agrees with R-free, data have some issues might be > particularly at the spot identification level! > What is the fraction of indexed vs unindexed spots reported by XDS- if you > run the following two lines? > > grep -c " 0 0 0" SPOT.XDS # gives non-indexed spots > > grep -vc " 0 0 0" SPOT.XDS # gives indexed spots > > Best, > Reza > > *____________________________________________* > *Md Rezaul (Reza) Karim, PhD* > Scientist II, Structural Biology > > > > > > On Wednesday, April 16, 2025 at 07:25:13 PM PDT, Stefan Clarke < > [email protected]> wrote: > > > Dear CCP4 Community, > > I was hoping for some insight into a problem I am having with crystal data > I collected. > > The data was auto-processed with XDS to 2.1Å with the I 1 2 1 space group > . (Unit cell dimensions - 47.39, 80.131, 160.433, 90, 98.3786, 90.) > Running Xtriage in phenix showed the data likely contain translational > pseudosymmetry however, Solvent and Matthews coefficient suggests there is > only one copy of the protein complex in the asymmetric unit. > > > I managed to find a molecular replacement (MR) solution in phenix (using > Phaser) for the protein complex and began refinements. The electron > density map looks good and in agreement with a 2.1Å dataset. However, the > refinement is stuck with high R-work and R-free values above 0.3 suggesting > there may be an issue with the space group of the XDS auto-processed data > or with the data. > > I re-processed the data using both HKL2000 and XDS. Both gave C 2 2 21 as > the space group (Unit cell dimensions - 47.458, 317.576, 80.126, 90, 90, > 90) and one copy of the complex is predicted to be in the asymmetric unit. > However, I have not been able to find a MR solution with this new space > group or its enantiomers using Phaser MR in phenix. > > Any suggestions and insight into this problem would be greatly > appreciated. If anything needs to be clarified, I’ll try my best to do so. > Thank you in advance. > > > ######################################################################## > > 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/ > > ------------------------------ > > 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/
