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 g...@globalphasing.com * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > ===============================================================
<<attachment: 3ftt-correl.png>>
