Re: [ccp4bb] Wilson B-factors recorded for all PDB's to 3.5Å

[sunanda williams]

Polygon in the validation tools of phenix.


On Saturday, October 15, 2016, amit sharma <
0d1d6aa5c57b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi,
>
> What is the average Wilson B-factor for all single crystal protein
> structures deposited in PDB at 3.5Å? Is there any software or a publication
> which could provide such an estimate?
>
> Thanks,
>
> Amit
>

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

[sunanda williams]

Quoting Dale from an older post
"It's also true that the Wilson B calculation assumes that all the B
factors in the crystal are the same - which is also far from the true in
most macromolecular crystals. A person who holds to the practice of
aggressively building water molecules and loops will create a model with a
higher average B than one who uses the same data but is more restrained.
The Wilson B will, of course, be unchanged.
If you have a protein that is equally ordered throughout and you do not
build in weak water molecules and the crystal diffracts high enough to
allow a reasonably accurate calculation of the Wilson B, your average B and
and the Wilson B should be close to each other. If your protein has mobile
loops, which most lower resolution crystals do (and most higher resolution
crystals for that matter) then your average B will be larger than your
Wilson B."

This kinda agrees with my scenario I think... Wilson B is 83 A*2 and Av B
98 A*2, the discrepancy contributed by mobile loops? (3.0 A resolution).
Refinement with group B factors (two per residue) brought the av B down to
80 A*2. TLS, PDB_REDO etc did not help much.
I got the model by Mol Rep, have not tried PROSMART...
And I agree with Phoebe...The aa's are fully there! Lowering the occupancy
may work with Hetatms, but doesn't make sense to do it with residues!




On Fri, Oct 14, 2016 at 9:08 PM, Phoebe A. Rice  wrote:

> Interesting way to look at it.  But those loop residues are really in the
> crystal with an occupancy of 1, so wouldn't letting the B factor fly give a
> clearer description of what's in the crystal?  Especially as many people
> know to color the structure by B factors to get a feel for which bits are
> wiggly, but they'll never think to color it by occupancy.
>
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthias
> Barone [bar...@fmp-berlin.de]
> *Sent:* Friday, October 14, 2016 8:00 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor
>
> Picking up the mail of Pavel, Phenix refines occupancies..
> If you expect the loops to be disordered, did you try to lower the
> occupancy of these residues, following Ethan Merritt statement that
> "general uncertainty [...] is represented better by occupancy <1 rather
> than an arbitrary large B factor" (To B or not to B,
> doi:10.1107/S0907444911028320).
> If this attempt does not bring the B-factors down, it will surely make the
> model more accurate, as the atom coordinates of the loops may not be
> correct at all, no?
>
> matthias
>
>
> >>> Pavel Afonine  14.10.16 9.36 Uhr >>>
>
> If you are still worry about your Bfactor, you could try TLS,
>>
>
> Or NCS, but SA with MLHL might be better.
>
> (A joke).
>
>

Re: [ccp4bb] High B factor

[sunanda williams]

Sorry for not making the problem clear!
The overall B factor for the 3.0 A structure is around 98.00 A*2. Most of
the deposited structures in the PDB site around this resolution
has an av B around 70 A*2
All other statistics looks fine. I got a warning message while trying to
upload the structure in PDB that 98 was higher than the norm!
The reason why the structure has such a high B factor could be due to
disordered loops... All the same I was wondering how acceptable this
structure would be to picky reviewers..
And 'better the B factors' means bring them down...sorry couldn't phrase it
'better'! I am going to try doing refinement with group B factors! Would
that help?
Thanks Robbie, I think this I need to make the best of the model I have.
Prof. Sekar will try PDB_redo..Thanks!



On Thu, Oct 13, 2016 at 11:41 AM, Pavel Afonine <pafon...@gmail.com> wrote:

> I fully agree with Dale in not understanding what the problem is. Perhaps
> I have a better chance if you clearly explain what exactly you mean by "is
> there any way to better the B factors".
> Pavel
>
>
> On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud <de...@daletronrud.com>
> wrote:
>
>>I'm sorry but I don't understand what your problem is.  Do you think
>> the B factors are too small for a 3A data set?  A range of 70 to 75 is a
>> little smaller than usual but probably not out of bounds.
>>
>> Dale Tronrud
>>
>> On 10/12/2016 7:59 PM, sunanda williams wrote:
>> > Hi all,
>> > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
>> > around 98. The B value is especially high at the N terminus and two loop
>> > regions (around 120-150 AA).
>> > The rest of the structure averaged around 70-75. Has anyone faced such a
>> > scenario? How reliable is the structure and is there any way to better
>> > the B factors.
>> > Any help is appreciated.
>> > Thank you!!
>>
>
>

[ccp4bb] High B factor

[sunanda williams]

Hi all,
I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
around 98. The B value is especially high at the N terminus and two loop
regions (around 120-150 AA).
The rest of the structure averaged around 70-75. Has anyone faced such a
scenario? How reliable is the structure and is there any way to better the
B factors.
Any help is appreciated.
Thank you!!