Dear Jacob, An R-value of 17% is indeed suspiciously high for a small molecule structure. Some thoughts:
Are you sure the space group is correct? There might be twinning involved,. Have you checked the ’signs of twinning’ for small molecules? There might be disordered solvent molecules, which could be modeled, although that’s not always trivial nor possible. How high are the residual peaks? This could give you info about what’s out there? If the residual peaks are located very close to heavy atoms, the data might suffer (severely) from absorption. Regards Kristof > On 3 Jun 2021, at 20:49, Jacob Summers > <000060a137e4bf3a-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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, 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/
