Dear Vonrhein, On Fri, Jul 31, 2009 at 12:47 AM, Clemens Vonrhein < [email protected]> wrote:
> Dear Jiamu, > > On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote: > > I am refining a structure of a complex between of 50kD protein and a 20kD > > glycosylated protien. The data is of 2.9 A resolution. The wilson B > factor > > is as high as 86.3 A^2. > > The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is > extra > > high. For the 50kD part, the average B factor is 76.5 A^2. But the B > factor > > of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the > > electron density looks fine, even the sugar chain is seen clearly. > > My question is: > > 1. How to reduce the B factor to a reasonable level? > > How do you define 'reasonable'? And why would you want to reduce this > anyway? > > ( 50*76.5 + 20*133.3 ) / 70 = 92.7 > > which seems fairly close to the Wilson B of 86.3, right? SO, the B value is right. > > 2. If it can not be redueced, when I published it, is this value > acceptable? > > Better question: is it the right value? Remember it is > > results -> publish > > and not > > publish <- results > > ;-) > > If they're correct than they are acceptable (I would accept those > values). You can accept these values. But I am not sure that you will be my reviewer certainly. Someone else can not accept. This is the key point. > > > > 3. In the same of similar resolutionIs, is there some other structures > like > > this situation? A component or a subunit of the protein has a extra high > B > > factor as high as 130. > > I'm sure hundreds of them ... but I'm sure you want your structure to > stand on its own, so don't look too close at other structures and > repeat the various mistakes we've all made and that are now set in > stone in some old PDB file. Thanks for your comments and best wishes. This is a great sustainment for me. > > > Cheers > > Clemens > > -- > > *************************************************************** > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * > * Global Phasing Ltd. > * Sheraton House, Castle Park > * Cambridge CB3 0AX, UK > *-------------------------------------------------------------- > * BUSTER Development Group (http://www.globalphasing.com) > *************************************************************** > -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [email protected]
