There's nothing wrong with translational NCS. It is what it is ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile -------- Original Message -------- On 29 May 2024, 15:49, Kay Diederichs wrote: > Hi Catherine, I think you meant to write "giving high R-factors". To add to > what Esko and Eleanor wrote: There is nothing wrong with your data or > spacegroup or refinement; it is just that the tNCS produces two sets of > reflections: half or your reflections are statistically "normal" (as if no > tNCS were there), and the other half is quite weak (their intensities would > be zero if the translation were 0,-0.5,0.5 which is not far from > 0.072,-0.498,0.5). As a result, one half of your reflections has a relatively > good agreement of Fcalc and Fobs; the other half agrees relatively worse > because a) they have less weight in refinement, b) their measurement error is > relatively higher than that of the strong reflections. The R-factor > calculation knows nothing about this, it just uses all reflections and so you > get something like an average R-factor which is of course higher than that of > the strong half. I'd say just document this in the paper you write about the > structure. It would be useful/interesting for such cases to have a program > that calculates R-values separately for the two classes of reflections (it > should be possible to do this with a script that employs CCP4 sftools, I > think). HTH, Kay On Wed, 29 May 2024 13:48:46 +0000, Catherine Back wrote: > >Hi, > >I have collected data for a protein which solved easily to 1.6 � > using MR. However, during data analysis and refinement it clearly has > translational NCS. According to Xtriage on Phenix: >Frac. coord.: 0.072, > -0.498, 0.5 >Distance to origin: 68.798 >Height relative to origin: 51.479% > >p-value (height): 5.577e-05 > >Wilson value and L-test suggests no twinning. > > >It solved using Molrep in ccp4i2. P2 21 21. All stats look good, but even > after refinement (not fully and completely finalised yet) R= 0.24 and > Rfree=0.27. Also, it appears the 2 molecules in the AU have swapped a helix > with their respective symmetry partners. I'm pretty sure I now have the > correct space group, and tried various others with much less success. > > > > 1. >Will these Rfactors be 'good'/low enough to publish for a dataset at > 1.6�? > 2. >Should I be doing anything else during structure solving to > alleviate the effects of tNCS? (I did try using Phaser to solve the > structure, but the stats were much worse and even though 'tNCS is present > correction factors were not applied'. I'm not sure why. > >Many thanks, >Cat > > > >Dr Catherine R. Back (she/her) > >Senior Post-doctoral Research > Associate > >School of Biochemistry > >University of Bristol > >UK > > > > > >######################################################################## > > >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 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 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/
