[sharp-discuss] Heavy atom density

[esserlo at helix.nih.gov]

> Why not to try refinement of everything, including HA occupancy, with
> direct SAD data in Refmac? If your mercury dataset is better than native,
> then it is likely (I am guessing) that you will use it for final
> refinement, right? At this point you have good phases already so native may
> be of limited use to you anyway.
>
> Artem

  Hi,

     apologies to Mark for duplication of my reply.

  My interest lies in the unmodified native data despite lower resolution. Hg
has bound to two CYS residues that are in active sites and i want the
structure without them. Perhaps this is part of the problem that the native
is obviously non-isomorphous (not very much so) to the derivative but I do
get quite decent PP and FOM and I think Sharp has a way to deal with
non-isomorphism as well as it can be done.

I was wondering if there is something I need to do or forgot to do to lower
(if not completely suppress) a spillover from Hg.

Ah, I have never used Refmac (in a serious way) - what is this Direct SAD
option ?

Thanks,

Lothar




>
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>
> On Mon, May 11, 2015 at 9:00 AM, <esserlo at helix.nih.gov> wrote:
>
>> Hi,
>>
>>    it's probably been too long that I did a full-fledged experimental phase
>> determination, which might explain my puzzlement over the following
>> observation:
>>
>> In my SIRAS case, with a good native but still better Hg derivative data
>> set
>> to resolutions of about 3.7 and 3.3 A respectively, I do get pretty good
>> experimental phases with Auto Sharp 2.8.1 SUSHI 3.10.1. So I am happy.
>> However
>> in density modification and later on in refinement that includes
>> experimental
>> phases (HL coefficients) I do get petty strong features for the Hg atom
>> sites.
>> Since there are bulky residues in the vicinity, there is a tendency for
>> them
>> to move into the strong ghost sites of Hg. Without experimental phase
>> support,
>> things clear up (no pseudo Hg density, obviously) but I would say that
>> overall
>> refinement clearly benefits from having experimental phases around.
>> {Refinements were done in BUSTER and Phenix with pretty much the same
>> effect}
>>
>> Maybe I am picking up the wrong coefficients ? I did use HLA-D from Sharp
>> which are the description of the calculated phase probability and my
>> understanding is that this is the right set to use. I am aware of the
>> documentation that speaks of phases with average heavy atom contribution
>> like
>> PHIBshasol but there is also PHIcentshasol which is "light atoms only". I
>> tried all of them (with and without average heavy atom contribution ) in
>> ccp4
>> DM: Density modification and averaging clearly have beneficial effects,
>> but I
>> still see pronounced density stemming from Hg. No matter what I do.
>>
>> Well, is this to be expected that even the "light atoms only" phase contain
>> information about the position of Hg atoms?
>>
>> Any suggestions ?
>>
>> Thanks,
>>
>>    Lothar
>>
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>