It's also possible that a lower Rfree is the result of reduced overfitting, because increased solvent content pushes up the obs/param ratio, i.e. the unit-cell volume is greater so you get more reflections for a given resolution cutoff, while the no of parameters stays about the same (i.e. there's a greater volume of solvent but you use the same no of parameters to describe it). Of course this assumes you get data to the same resolution with the increased solvent content, which may not be the case if there's increased thermal motion/disorder.
Cheers -- Ian On Tue, May 24, 2011 at 10:01 AM, <[email protected]>wrote: > This is not my experience. Provided the solvent is featureless, I find > that a high solvent contents leads to a lower Rfree due to a kind of > solvent flattening effect. Of course, if a significant part of the > molecule(s) is/are disordered, this will lead to a degradation of the > Rfree. > > My 2 cents, > Herman > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Clement Angkawidjaja > Sent: Tuesday, May 24, 2011 10:47 AM > To: [email protected] > Subject: Re: [ccp4bb] how to remove part of data with bad signal to > noise ratio > > Hi Seema, > > Small addition to the already abundant suggestions, if you have high > solvent content or significant portion of non-observable density, you > normally get higher R-free. > > Clement > > #################################################### > Clement Angkawidjaja, PhD. > G30 Assistant Professor > ------------------------------------------------------------------------ > ------------------- > Chemistry-Biology Combined Major Program International College, Osaka > University 1-30 Machikaneyama-cho Toyonaka, Osaka 560-0043, Japan > http://cmp.sci.osaka-u.ac.jp/CMP/ Tel. +81-6-6850-5952 Fax > +81-6-6850-5961 > ------------------------------------------------------------------------ > ------------------- > Laboratory of Molecular Biotechnology > Graduate School of Engineering Osaka University > 2-1 Yamadaoka U1E-804 > Suita, Osaka 565-0871, japan > http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html > Tel/Fax +81-6-6879-4157 > #################################################### >
