Hi Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å data most small molecule crystallographers would do this as a first step after fitting all the non-H atoms.
One thing I can’t agree with is to cut the resolution of your data _unless_ you have a very, very good reason to do so. Normal small molecule refinements will use data to ~0.8Å and not use a cut-off based on resolution or I/sig(I). A good dataset will often go to higher resolution and small molecule crystallographers will be very happy to use these data (unless, as I say, they have a very good reason not to), and would certainly have to “explain to the referees” why they didn’t if they ignored a systematic chunk. Something else that you might not have thought of - have you actually told SHELXL what the reflection data are - i.e., are they F, F^2, intensity? It’s perfectly possible to solve a small molecule structure by e.g. telling the program you’re giving it F^2 but actually giving it F, but refinement would be somewhat less straightforward. SHELXL normally uses F^2 in refinement, macromolecular programs still normally use F (AFAIK). What programs did you use for processing the diffraction data? Of course, lowering the R factor is not the objective of the exercise - a lower R-factor is a consequence of having a model that fits the data better. I would be strongly inclined to ask a small molecule crystallographer (or someone with a strong background in it) to have a look at your data & model - they could probably give you a definitive answer by return of e-mail. Just my two ha’porth Harry > On 4 Jun 2021, at 03:10, Jon Cooper > <[email protected]> wrote: > > Agreed, ANIS is the command to try. > > Sent from ProtonMail mobile > > > > -------- Original Message -------- > On 3 Jun 2021, 20:18, Philip D. Jeffrey < [email protected]> wrote: > > 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 <[email protected]> on behalf of Jacob Summers > <[email protected]> > Sent: Thursday, June 3, 2021 2:49 PM > To: [email protected] <[email protected]> > 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, 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 ######################################################################## 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/
