R1 of 17% is bad for small molecule. 0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs then these might be too aggressive for small molecule-type refinement stats - try a more conservative cutoff lie 0.9 and see how that changes R1. However I suspect it's more to do with how your model is fitting the data.
Have you refined anisotropic Bfactors ? Have you added hydrogens ? I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface for the refinements - I use the latter and it's somewhat Coot like with useful features that are particular to small molecule. Also PLATON has some things (like expand-to-P1 and Squeeze) that, respectively, might be useful to explore space group issues and disordered solvent. PLATON also has a means to check for some forms of twinning. Phil Jeffrey Princeton ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jacob Summers <000060a137e4bf3a-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, June 3, 2021 2:49 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Lowering R factor from small molecule structure Greetings! I am currently trying to reduce the R factor of a cyclic small molecule peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. The molecule itself fits the density very well, but there are a few unexplained densities around the molecule which do not seem to be anything in the crystallization conditions. The R1 factor of the refinement is 17.07% but I am unsure how to lower this value. Any ideas on how to better refine this molecule or fill densities to lower the R1 factor? I do not have much experience working with small molecule refinement or with ShelX. Thanks so much, Jacob Summers ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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/
