Dear John,
We’ve had good success placing fragments with Phaser to solve Fab structures, along the lines that a number of people have mentioned already.
In terms of your original question about weak data, the version of Phaser in current releases of CCP4 and Phenix now accounts much better for the effect of intensity measurement errors. (But make sure you give it intensities and particularly not French&Wilson amplitudes!) If you have a good partial model, data to the highest possible resolution will help, and — as long as the intensity sigmas are reasonably accurate — pushing the resolution shouldn’t hurt. However, it’s probably fair to say that when the resolution limit is pushed to extremes, the integration and scaling programs do a poorer job of estimating the standard deviations.
Best wishes,
Randy
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> On 2 Jun 2016, at 10:55, John R Helliwell <[log in to unmask]> wrote:
>
> Dear Colleagues,
>
> We would be grateful for suggestions on the following case of molecular replacement using antibody H and L chains (ie high percentage of beta sheet content) and weak X-ray diffraction data ie going to 3.2 Angstrom (<I/sigI> crossing 2), 2.8 Angstrom (CC½ crossing 0.25) and finally processed to 2 Angstrom where the molecular transform (presumably) rises again to give a CC½ 0.04. We recall that beta sheet protein subunit placements can prove awkward, due presumably to the hydrogen bonding electron density, running perpendicular to the polypeptide chains, preventing a successful placement.
>
> So, are there particularly successful MR programs or specific, non-default, MR program settings for such a case?
>
> Thank you,
>
> John and Emmanuel
>
>
>
> John R Helliwell & Emmanuel Saridakis
|