Re: [ccp4bb] B-factor & Space gr questions!

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From: Jeff Lee jlee {- at -} SCRIPPS {- dot -} EDU
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Subject: Re: B-factor & Space gr questions!
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-05

Subject: Re: B-factor & Space gr questions!
From: David Briggs bassophile {- at -} GMAIL {- dot -} COM
Date: 2007-06-05

Hi Ibrahim,

On 04/06/07, Ibrahim M. Moustafa wrote:
>
> Hi all,
>
> While reading a crystallographic paper describing the structure
> of an apo-protein and its complex I noticed that
>
> the authors described the space goup as P6122 for the unit cell:
> a=141.9, b=143.9, c=380.4
> Could this be considered as a typo or I'm missing something here!
> the requirement for the hexagonal is a = b # C....right?

You are correct, for Hexagonal, a=b - so It's got to be a typo - data most
processing software wouldn't let you do this.

Another observation in that paper too: the B-factors for the 2.4 A
> and 3.2 A structures are 39 and 40?? Does this make sense to anyone?

They're quoting Wilson B-factors, I imagine. A small but rather important
difference - where was this published?

The last question: In the same paper, for the complex structure R and
> Rfree are equal (30%) is that an indication for improper refinement
> in these published structure? I'd love to hear your comments on that too.

Well, it certainly is a little suspicious looking - I've had similar
experiences to Ed, regarding similar R & Rfrees from rigid rigid body
refinement prior to positional refinement. Have the authors deposited the
Structure factors? I would use EDS to check the maps out: eds.bmc.uu.se/eds/

thanks,
> Ibrahim

HTH, Dave

--
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David Briggs, PhD.
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www.dbriggs.talktalk.net
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CCP4bb <-- 2007 <-- June 2007 <-- 05 June 2007

Previous message:
Subject: Error/Bug in Pirate?
From: Jeff Lee jlee {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-04

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Subject: Re: B-factor & Space gr questions!
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-05