[phenixbb] Anomalous or not?

[Oganesyan, Vaheh]

Shouldn’t phases from MR be a better way to look for bromated ligand in Fo-Fc maps in such a case?



Regards,

Vaheh
8-5851

From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of CPMAS Chen
Sent: Thursday, July 10, 2014 12:53 PM
To: Ryan Spencer
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Anomalous or not?

Well, let me make this clear.

1. I am using Br anomalous signal to identify the potentially bound ligand.
2. I do shoot the crystals at 0.92A.
3. the different crystals have different resolution, but anomalous signal was weak as reported by autoxds.

Charles

On Thu, Jul 10, 2014 at 12:25 PM, Ryan Spencer <rspencer at uci.edu<mailto:rspencer at uci.edu>> wrote:
So I assume you were not able to shoot the crystal at ~0.92 A at SSRL or are the crystals sensitive? If you were limited to the single wavelength beam which is around 1A you’re dealing with a really low f” of 0.5322. There have been crystals solved with Sulfur using an in-house Cu sources (takes a lot of merged sets and anomalous is stronger at certain crystal angles) which gives about the same anomalous scattering as Br. Is the bromine covalent or is it soaked ion?

Alternatives – soak with potassium iodide and get a dataset from an in-house source (iodine f” 6.6 at 1.54), or at least the anomalous locations. You may get a partial model to use for replacement at that point.

Did each processed dataset have the same level of anomalous signal when processed individually?

Ryan


From: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [mailto:phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>] On Behalf Of CPMAS Chen
Sent: Thursday, July 10, 2014 8:55 AM
To: Francis Reyes
Cc: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Anomalous or not?

Francis,

My anomalous plot for Br is more like your Cobalt 1 site less redundancy.

Ryan,

As my Br anomalous signals are weak, I merged signals from multiple crystals.

Meanwhile I am looking into the detail about the autoxds processing as suggested by Tim.

Thanks,

On Thu, Jul 10, 2014 at 10:02 AM, Francis Reyes <Francis.Reyes at colorado.edu<mailto:Francis.Reyes at colorado.edu>> wrote:
In addition to Tim's comments above, using loggraph to see the anomalous CC plot from scala is a good qualitative indicator of whether you have anomalous signal..


Some data points for what reasonable plots  (and their corresponding XDS SigANO's) look like: https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf


F

On Jul 10, 2014, at 9:03 AM, CPMAS Chen <cpmasmit at gmail.com<mailto:cpmasmit at gmail.com>> wrote:

>
> Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i.
>



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Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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