A small erratum is needed unfortunately. The sequence identity of 4UHV to 2P5Z is 19% (but not the exceptional 15% as I wrote originally). Nevertheless, Phaser successfully finding a solution for a 19% SI model is no small feat.
> On Mar 16, 2016, at 09:48, Petr Leiman <petr.lei...@epfl.ch> wrote: > > Dear Prof. Bricogne, > > As your statements carry a huge weight in this community, I have to mention > that exceptions to the rule you formulated exist. > >> On Mar 15, 2016, at 17:21, Gerard Bricogne <g...@globalphasing.com> wrote: >> >> Dear Smith, >> >> The only way to achieve such a low R-value at low resolution is >> to inject extra geometric restraints based on the knowledge of a very >> similar structure already refined against high-resolution data, e.g. >> the structure that was used to get an MR solution. > > Here is one example (3.3 A resolution and R-free of 19.5%): > http://www.rcsb.org/pdb/explore.do?structureId=4MTK > There is a caveat of course. High resolution here is mimicked by a very high > solvent content - 82% or 86%. > > Before anyone starts to suspect that this structure is based on a higher > resolution structure (PDB code 4UHV), I urge the unbelievers to inspect the > deposition and release dates on the two entries. Our structure was released > 1.5 years before the higher resolution structure was deposited… Also, please > check the refinement quality parameters of the two entries. > > Other notes: we solved our structure by MR using a homologous structure of a > fragment as a search model (PDB 2P5Z). The model represented 56% of the unit > cell content and had only 15% sequence identity. And amazingly Phaser worked > (thanks Randy Read!). The second remarkable thing was Resolve pulling density > out of ‘thin air’ using 6-fold averaging (thanks Tom Terwiligger!). In this > figure, panel A is the MR density and panel B is the 6-fold NCS-averaged map: > https://www.dropbox.com/s/kbf3b3c1lkdj3ph/Figure-S2.jpg?dl=0 > > We never published this because the focus of the paper has been changed > several times since the structure was solved. But the draft is 98% ready now, > so it will be published soon. > > Sincerely, > > Petr > > P.S. I can share the raw data if anyone is interested in examining this > dataset in detail. > > ------------------ > Petr Leiman > EPFL > BSP 415 > CH-1015 Lausanne > Switzerland > Office: +41 21 69 30 441 > Mobile: +41 79 538 7647 > Fax: +41 21 69 30 422 > http://lbbs.epfl.ch > > >> We have called this >> "targeting" - for a method of doing this, see >> >> Smart et al. (2008). Abstr. Annu. Meet. Am. Crystallogr. Assoc., >> Abstract TP139, p. 117. >> >> subsequently described in more detail in >> >> http://journals.iucr.org/d/issues/2012/04/00/ba5178/stdsup.html >> >> and the implementation of similar ideas in REFMAC using ProSmart (not >> the same Smart :-) ) . >> >> These "external restraints" try to preserve the local geometry of >> the target structure by keeping short internal interatomic distances >> in the structure being refined against low-resolution data as close as >> possible to what they are in the target structure. Phenix uses a >> similar idea, but based on imposing a similarity of torsion angles: >> >> http://journals.iucr.org/d/issues/2014/05/00/rr5054/stdsup.html >> >> An early and rather extreme way of doing this was to use the MR >> model in a rigid body refinement and be lucky enough that this MR >> model was spot on. >> >> Keeping track of the fact that such a targetting has been applied >> in a refinement, and how, (i.e. Dale's question about how such a model >> was created) is an obvious challenge in relation to deposition: if the >> use of this procedure is not recorded nor documented, you will get >> outliers with respect to the usual trends in R-values vs. resolution, >> just like the one you have spotted, and all the data mining of these >> trends will be messed up. >> >> >> With best wishes, >> >> Gerard >> >> -- >> On Tue, Mar 15, 2016 at 08:34:31AM -0700, Dale Tronrud wrote: >>> Without knowing the structure it is hard to make any comment. >>> Usually the only way to get an R value this low at 3.9 A resolution is >>> to start with a high resolution model and MR it into the low resolution >>> map. >>> >>> It is a good sign for the future of methods development that a good >>> model will fit a low resolution data set but we don't know how to CREATE >>> such a good model using ONLY the low resolution data set. >>> >>> Dale Tronrud >>> >>> On 3/15/2016 6:36 AM, Smith Liu wrote: >>>> Thanks Eugene. >>>> >>>> The paper I read was from a top journal. The resolution was 3.9, and the >>>> R-factor was 0.233. I was interested to know how to get Rfactor 0.233 >>>> from 3.9 A resolution map. >>>> >>>> Smith >>>> >>>> >>>> >>>> 在 2016-03-15 19:42:48，"Eugene Osipov" <e.m.osi...@gmail.com> 写道： >>>> >>>> Dear Smith, >>>> R-factors not the aim but indicators. My teacher taught me that with >>>> correct weighting scheme rmsd of bonds and angles in your model >>>> should be similar to rmsd's of monomers in library. So I try to keep >>>> weight which gives rmsd of bonds ~0.02 after refinement. Focus >>>> rather on correct description of your model in terms of chemical and >>>> physical sense. >>>> >>>> 2016-03-15 10:57 GMT+03:00 Smith Liu <smith_liu...@163.com >>>> <mailto:smith_liu...@163.com>>: >>>> >>>> Dear All, >>>> >>>> I just read a sentence " To prevent over-refinement, an >>>> appropriate weighting of the geometry versus the >>>> crystallographic term was established empirically, aiming >>>> at good model geometry with a low R value". By CCP4 refmac >>>> refine, will you please let me know which strategy are helpful >>>> for getting lower R value? >>>> >>>> Smith >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Eugene Osipov >>>> Junior Research Scientist >>>> Laboratory of Enzyme Engineering >>>> A.N. Bach Institute of Biochemistry >>>> Russian Academy of Sciences >>>> Leninsky pr. 33, 119071 Moscow, Russia >>>> e-mail: e.m.osi...@gmail.com <mailto:e.m.osi...@gmail.com> >>>> > > >
