[phenixbb] few questions about resolving new structure through MR

Nathaniel Echols nechols at lbl.gov
Thu Nov 7 09:05:57 PST 2013

On Thu, Nov 7, 2013 at 8:34 AM, Zhihong Yu <nkyuzhih at gmail.com> wrote:

> 1. Is it possible to find a resolution through MR approach using
> structureX as a search model? Especially considering that the resolution is
> only 3.5Å. Currently I just tried once using phaser and refine the
> structure for 3 cycyles, I can get a R/Rfree of 0.45/0.55, and it looks
> like most of backbone in the structureX, especially those within helix or
> sheet, can be well described by 2Fo-Fc density. Is this primary result
> promising or not?

No, that's a classic example of model bias.  Positive (and continuous)
mFo-DFc density outside of the placed atoms is what you should be looking
for, but I suspect there will be very little.  It's basically impossible to
tell from this result whether the placement of structureX is even correct,
although the Phaser statistics may be informative.

One unrelated suggestion: given the low sequence identity, I think it will
be very important to properly prepare the input model (use Sculptor for

2. If it’s possible, what’s the general optimal procedure I should follow?

I confess I haven't had to solve a structure like this myself - just seen a
bunch of datasets where similar attempts didn't work - but it's hard to see
how it can be solved without experimental phasing information (SeMet,
etc.).  The good news is that if you can get a correct MR solution for
domainB, you can use MR-SAD to find heavy atom sites and solve the
structure, which should be easier than starting from no phases at all.

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