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Subject:

Re: Ca or Zn

From:

Armin Wagner <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Thu, 1 Nov 2012 21:30:12 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

 
Dear John, 
 
Thanks for pointing to the long-wavelength MX beamline project here at Diamond. 
 
The core wavelength range will be from 3 to 8 keV (1.5 to 4.1 A) and mainly targeting anomalous phasing experiments from native proteins/DNA/RNA exploiting anomalous differences from S or P. But of course, the energy range will allow to unambiguously determine cations such as K+ or Ca++.  
 
We have just started X-ray commissioning of the beamline optics and will expect first users from autumn 2013. 
 
Best regards, 
 
     Armin 
 
 
-----Original Message----- 
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Jrh 
Sent: 31 October 2012 08:20 
To: ccp4bb 
Subject: Re: [ccp4bb] Ca or Zn 
 
Dear Ethan, 
Yes indeed.  
An exciting development underway at Diamond Light Source led by Armin Wagner will greatly improve the ease of measurement at eg the calcium edge but also extending that wavelength range. The  furin paper I quoted  did nevertheless successfully show structural detail from those measurements. 
 
The Ga and Zn edges wavelengths are an easier challenge to access, i agree of course, rather the interest I tried to stress was the getting of the sigmas on the occupancies as well as the occupancies themselves, and how we did that and checked them via more than one software is also hopefully of interest. 
 
Greetings from Taipei, 
John  
 
Prof John R Helliwell DSc  
  
  
 
On 31 Oct 2012, at 10:37, Ethan Merritt <[log in to unmask]> wrote: 
 
> On Tuesday, 30 October 2012, Jrh wrote: 
>> This paper describes use of data either side of the calcium edge:- 
>>  
>> http://dx.doi.org/10.1107/S0907444905002556 
>  
> I think that counts as "not amenable" (which is not quite the same as  
> "impossible".  From the Methods section of that paper: 
>  
>  Measurements in the vicinity of the K absorption edge of  calcium  
> (3.07 Å) are close to or beyond the physical limit  of most beamlines  
> typically used for X-ray crystallography  [...] It was not possible to  
> observe interpretable  diffraction patterns at λ >= 3 Å with the  
> weakly diffracting  furin crystals using the MAR CCD detector and  
> exposure  times up to 20 min per degree of rotation. 
>  
> They did soldier on and managed to collect extremely weak data below  
> the Ca edge and stronger but still very weak data above the edge where  
> the Ca f" term was appreciable.  But this is far from a routine  
> experiment. 
>  
> Another approach dating back to work in 1972 by Peter Coleman and  
> Brian Matthews http://dx.doi.org/10.1016/0006-291X(72)90750-4 
> is to replace the Ca with a rare earth having similar chemistry (e.g.  
> La, whose L-1 edge is at 1.98Å). 
>  
>  
>> This next paper describes a case of gallium and zinc mix at one site  
>> with occupancy AND sigmas estimated with different software. 
>> This example is however much better diffraction resolution than that  
>> you may have. But hopefully will still be of interest:- 
>> http://dx.doi.org/10.1107/S0108768110011237 
>  
> Ga and Zn, sure.  That's an easy one.  
> The Ga edge is at 1.196Å and the Zn edge is at 1.284Å, both edges are  
> nicely in range for data collection and they are close enough together  
> that little or no beamline readjustment is needed when jumping from  
> one to the other. 
>  
>    Ethan 
>  
>  
>  
>>  
>> Prof John R Helliwell DSc 
>>  
>>  
>>  
>> On 31 Oct 2012, at 04:53, Ethan Merritt <[log in to unmask]> wrote: 
>>  
>>> On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote: 
>>>  
>>>> The coordination is indicative but not conclusive but, as I  
>>>> responded to the original poster, I think the best approach is to  
>>>> use anomalous scattering.  You can measure just below and above the  
>>>> Ca edge, 
>>>  
>>> Actually, you can't.  The Ca K-edge is at 3.07Å, which is not a  
>>> wavelength amenable to macromolecular data collection. 
>>>  
>>>   cheers, 
>>>  
>>>       Ethan 
>>>  
>>>  
>>>> and similarly with the Zn, and those maps will be _highly_ indicative of the relative amounts of metal ion present.  In fact, you can deconvolute so that you know the occupancy of the metals at the various sites. 
>>>>  
>>>> Adrian 
>>>>  
>>>>  
>>>> On 30 Oct 2012, at 22:37, Chittaranjan Das wrote: 
>>>>  
>>>>> Veerendra, 
>>>>>  
>>>>> You can rule out if zinc has replaced calcium ions (although I agree with Nat and others that looking at the coordination sphere should give a big clue) by taking a few crystals, washing them a couple of times and subjecting them to ICP-MS analysis, if you have access to this technique. You can learn how many zinc, if any, have bound per one protein molecule in the dissolved crystal. 
>>>>>  
>>>>> Best 
>>>>> Chitta 
>>>>>  
>>>>>  
>>>>>  
>>>>> ----- Original Message ----- 
>>>>> From: "Veerendra Kumar" <[log in to unmask]> 
>>>>> To: [log in to unmask] 
>>>>> Sent: Tuesday, October 30, 2012 2:55:33 PM 
>>>>> Subject: [ccp4bb] Ca or Zn 
>>>>>  
>>>>> Dear CCP4bb users, 
>>>>>  
>>>>> I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites.  I purified the protein  in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or  zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions?  
>>>>> is there any way we can find the electron density value at different peaks?  
>>>>>  
>>>>> Thank you 
>>>>>  
>>>>> Veerendra 
>>>>  
>>>  
>>  
>  

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