Many thanks to all who replied, and thank you for your insight and advice. I'll make sure I add a bit in the SI that explains why the R-factors are high.
Kay - yes, apologies I did mean 'high' R factors lol. Andy - both molecules in the AU are well defined. Best wishes, Cat Dr Catherine R. Back (she/her) Senior Post-doctoral Research Associate School of Biochemistry University of Bristol UK catherine.b...@bristol.ac.uk ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> Sent: 29 May 2024 16:30 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors 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 < kay.diederi...@uni-konstanz.de> 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 ######################################################################## 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/
