Dont forget the confusing interaction between recorded B factors in a
PDB file and TLS parameters. This Q is still I think unresolved but you
need to be careful!
Eleanor
Edward A. Berry wrote:
Interesting that the correlation between B-factor and
resolution didn't show up in the QDB as recentl
Interesting that the correlation between B-factor and
resolution didn't show up in the QDB as recently as 2001.
Or am I missing something?
From what i understand this includes structures with
resolution from 1.5 to 3.5 A.
On Jan 4 2001 Gerard "CD" Kleywegt wrote:
well, i had a quick look at the
Hi,
On Fri, Jul 31, 2009 at 09:32:02AM +0800, Jiamu Du wrote:
> > 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.
I don'
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Pavel Afonine
> Sent: 31 July 2009 03:39
> To: Jiamu Du
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] question of extra high B factor
>
>
Hi Pavel,
these are interesting tables ... but am I right that the low-B,
low-resolution structures in your 1st and 2nd table are fairly old -
refined at a time when crystallographers still thought that high B
factors should raise eyebrows?
Could it be that those structures that were refined
Dear Afonine,
Thanks for your kind help.
Best wishes.
On Fri, Jul 31, 2009 at 10:38 AM, Pavel Afonine wrote:
> Hi,
>
>all the errors go into B and so you can get decent R with wrong
>> structure. Glycosylated proteins have a large component totally disordered -
>> do you see any sugars?
>>
Hi,
all the errors go into B and so you can get decent R with wrong
structure. Glycosylated proteins have a large component totally
disordered - do you see any sugars?
with B~133 you uj is 3.7A which means that atom is all over the
place and meaningless
As a reviewer I wo
Dear Vonrhein,
On Fri, Jul 31, 2009 at 12:47 AM, Clemens Vonrhein <
vonrh...@globalphasing.com> 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
-
> *From:* Jiamu Du [mailto:jiam...@gmail.com]
> *Sent:* Thu 7/30/2009 12:15 PM
> *To:* Skrzypczak-Jankun, Ewa
> *Subject:* Re: [ccp4bb] question of extra high B factor
>
> Dear Dr. Ewa,
> I have checked the data with Phenix. It is not a twin. I think the
On 00:00 Fri 31 Jul , Jiamu Du wrote:
> Dear All,
> 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-fact
Jiamu Du schrieb:
Dear All,
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 50k
I am using TLS refinement with Phenix for the structure refinement.
On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du wrote:
> Dear All,
> 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
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 0.21/0.2
Hi Jiamu,
My question is:
1. How to reduce the B factor to a reasonable level?
3. In the same of similar resolutionIs, is there some other structures
like this situation?
POLYGON tool is (one of) your friend(s) to answer this question (apart
from debatable one about "a reasonable level"):
Dear All,
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 f
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