Re: [ccp4bb] Checking for gremlins in deposited diffraction data (with plot)

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Checking for gremlins in deposited diffraction data
From: Gerard Bricogne gb10 {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-03-06

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Subject: Re: Checking for gremlins in deposited diffraction data (with plot)
From: Gerard Bricogne gb10 {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-03-06

Dear all,

This time, with plot attached - and apologies.

Gerard.

--
On Fri, Mar 06, 2009 at 05:58:49PM +0000, Gerard Bricogne wrote:
> Dear all,
>
> The newly-deposited structure 3ftt from the CSGID structural genomics
> group has fields in its sf.cif file called F_meas_au and F_meas_sigma_au,
> but which clearly contain F_calc and ph_calc - at least, the F_meas_sigma_au
> field is uniformly distributed on [0,360] and the F_meas_au field has a >90%
> correlation with the calculated structure factors from the deposited PDB
> file in all resolution bins.
>
> Thomas Womack's routine re-refinement of all structures deposited each
> week picked this up through a final Rfree value of 47% and a difference map
> with points at both +35 sigma and -35 sigma. His manual inspection of the
> difference map indicated negative density at every oxygen and nitrogen atom,
> and a more in-depth look at the structure factors picked up the root cause.
> The link between that cause and its effect on the final Rfree was explained
> by the fact that the erroneous sigma values resulted in very small F/sig(F)
> values at high resolution, hence in a very high value of the refined Luzzati
> B factor produced by BUSTER-TNT, and an anticipated decorrelation between
> expected and observed amplitudes. The attached reciprocal-space correlation
> coefficient plot showed this very clearly.
>
> This instance leaves room for some concern about the verification of
> deposited structure factors: what happened here is consistent with the
> hypothesis that the standard-deviation field is ignored entirely, or at
> least that no plausibility check is carried out on the values deposited in
> it.
>
>
> With best wishes (and thanks to Thomas Womack),
>
> Gerard.
>
>
> --
>
> ===============================================================
> * *
> * Gerard Bricogne gb10@GlobalPhasing.com *
> * *
> * Global Phasing Ltd. *
> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
> * *
> ===============================================================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Checking for gremlins in deposited diffraction data
From: Gerard Bricogne gb10 {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-03-06

Next message:
Subject: problem restraining angles formed between cysteine and a ligand
From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2009-03-06