Well, wouldn't NCS be a parallel situation? I have heard, for example, that the maps of viruses are considerably better at a given resolution than monomeric proteins. So I would guess that someone has looked at this topic in the case of NCS. Maybe high solvent content would be equivalent to filling the solvent holes with equivalent proteins (assuming (unrealistically) that the crystal diffract to the same resolution, since the parameter ratio would be the same?
JPK On Fri, Mar 15, 2013 at 9:27 AM, Guangyu Zhu <g...@hwi.buffalo.edu> wrote: > Ian, > > Because it is same protein, the high thermal motion is likely caused by > crystal packing, and should be corrected by TLS refinement. The B left over > should be similar. > > Anyway, this is just a hypothetical question. I tried to make other things > same and just compare resolution and d/p. But you can still find > difference. So if 80% crystal diffract to 3.0A too, then d/p ratio is much > higher than 3.0A 50% crystal, it must be a more accurate refinement. What > if 80% crystal diffract to 3.1, 3.2A, or 3.3A? Or I change the question to: > could d/p ratio compensate some resolution? > > Thanks! > Guangyu > > From: Ian Tickle <ianj...@gmail.com> > Date: Friday, March 15, 2013 6:33 AM > To: System Administrator <g...@hwi.buffalo.edu> > Cc: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk> > Subject: Re: [ccp4bb] Resolution and data/parameter ratio, which one is > more important? > > > Hi Guangyu, > > I think it's not as straightforward as comparing d/p ratios, that is only > one of several factors that influences precision. Another important factor > would be the overall level of thermal motion & disorder which will most > likely be significantly higher in the 3.6A 80% case; after all that's > probably the reason that it only diffracts to 3.6A! > > All things considered I would go for the 3A form. > > Cheers > > -- Ian > > > On 15 March 2013 00:27, Guangyu Zhu <g...@hwi.buffalo.edu> wrote: > >> I have this question. For exmaple, a protein could be crystallized in two >> crystal forms. Two crystal form have same space group, and 1 >> molecule/asymm. One crystal form diffracts to 3A with 50% solvent; and the >> other diffracts to 3.6A with 80% solvent. The cell volume of 3.6A crystal >> must be 5/2=2.5 times larger because of higher solvent content. If both >> data collecte to same completeness (say 100%), 3.6A data actually have >> higher data/parameter ratio, 5/2/(3.6/3)**3= 1.45 times to 3A data. For >> refinement, better data/parameter should give more accurate structure, ie. >> 3.6A data is better. But higher resolution should give a better resolved >> electron density map. So which crystal form really give a better (more >> reliable and accurate) protein structure? >> > > -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
