Rerun truncate on your data ans look at the graphs - they often give
clues if the <I> distribution is distorted..
Eleanor
PS - maybe we are a nervous lot, but we always re=process synchroton
data again at home with time to think about it..
James Pauff wrote:
> Hello all, thank you for the responses. Just to clear up a couple of things...
> 1) My dataset was acquired on a synchrotron and scaled/truncated there. To my knowledge they used the same procedure as for other structures that we have obtained there...which have had no B factor issues. Granted, our modified protein is of a different spacegroup than previous.
>
> 2) I have not used/touched the TLS parameters at all.
>
> The idea that our 73% completeness (thus lacking 27% of the 'weakest' reflections) has lead to an artificially low B factor sounds most appealing at this point?
>
> As usual, I greatly appreciate all of your insights here!
>
> Best,
> Jim
>
>
> --- On Wed, 8/20/08, Eleanor Dodson <[log in to unmask]> wrote:
>
>
>> From: Eleanor Dodson <[log in to unmask]>
>> Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...
>> To: [log in to unmask]
>> Cc: [log in to unmask]
>> Date: Wednesday, August 20, 2008, 4:30 AM
>> James Pauff wrote:
>>
>>> Hello all,
>>>
>>> I have a refined structure at 2.6 angstroms that at
>>>
>> about 73% completeness at this resolution. The I/sigma is
>> about 2.0 at 2.6 angstroms, and the omit density for my
>> ligands is great contoured at 3.0sigma. My Rcryst is 19 or
>> so and the Rfree is 24.5 or so.
>>
>>> HOWEVER, my mean B value is 13.9, whereas my other 2
>>>
>> structures (at 2.2 and 2.3 angstroms, same protein, >95%
>> completeness) have mean B values of 22+. Any suggestions as
>> to what is going on here? I'm having trouble explaining
>> this.
>>
>>> Thank you,
>>> Jim
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>> Have you used TLS - listed B factors will then be given
>> relative to the
>> TLS parameters. You need to run tLSANL to get a more
>> realistic value.
>> Eleanor
>>
>>
>> But in fact temperature factors are rather harder to
>> estimate at lower
>> resolutions than higher. Look at your <Fo> and
>> <Fc> curves v resolution
>> ( part of a REFMAC loggraph) and you can see that sometimes
>> the overall
>> scaling struggles to get a reasonable fit..
>>
>
>
>
>
>
>
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