[ccp4bb] DLS/CCP4 data analysis workshop 2017

[David Waterman]

PhD students, postdocs and early career scientists,

Please consider applying for the fourth joint DLS/CCP4 workshop on MX data
collection and structure solution, to be held at Diamond Light Source, UK
from the 30th November to the 7th December 2017.

This course offers the opportunity for you to work alongside leaders in the
field of MX on data from your own crystals. For more details please check
here:

http://www.ccp4.ac.uk/schools/DLS-2017/

The application period is now open and will close on the 6th October.
Applicants will be required to submit a CV/resume, describe their projects
and obtain a letter of support from a supervisor, so please do not wait
until the last minute to apply! Those with crystals and/or data will be
given priority.

Best wishes on behalf of the organisers,

David Waterman (CCP4)

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

[Robbie Joosten]

...I would not recommend trying that.

Sorry for the fat finger,
Robbie

Sent from my Windows 10 phone

From: Robbie Joosten
Sent: 12 September 2017 21:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?


Liquid mercury cannot be absorbed very well through the skin. Also ingestion 
seems to be much less risky than breathing in mercury vapours. My 
thermodynamics lecturer at uni was convinced that you can drink liquid mercury 
with no health risk, but I would not rec



Sent from my Windows 10 phone



From: George Sheldrick
Sent: 12 September 2017 20:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?



Over 50 years ago, a Toepler pump that I had glass-blown myself
developed a crack that caused several kilos of mercury to hit tha
ceiling and give me a shower. Fortunately I did not then know how
poisonous it was and suffered no ill-effects

George


On 12.09.2017 19:46, James Holton wrote:
> One more correction,
>
> It seems brominated vegetable oil (BMO) really does contain Br atoms!
> I could have sworn I read in some reputable source long ago that the
> process of "bromination" was an old term for general reduction of
> double bonds and did not necessarily involve bromine. Usually
> hydrogen.  I remembered this because I thought it was hugely
> counter-intuitive.  Now, of course, I cannot find that reference. So,
> who am I to pit the validity of my memory against Wikipedia and a long
> list of links to health-nut web blogs?  Guess I was wrong about that.
>
> The Mountain Dew I am drinking right now has a very faint X-ray
> fluorescence peak that could be Br.  Hard to be sure above
> background.  So I will have to get a sample of neat BMO to sit next to
> my shampoo, pepto and sunscreen on my shelf of heavy atom compounds
> that are on the FDA's GRAS list:
> https://www.fda.gov/food/ingredientspackaginglabeling/gras/
>
> Remarkably, the MSDS for BMO is less scary than that of ordinary
> vegetable oil.  This raises more than one interesting topic, but the
> most relevant here I think is "bio-availability". Selenomethionine is
> much much more bioavailable than selenium sulfide, which is the active
> ingredient in my dandruff shampoo. Apparently, humans don't absorb it,
> but microorganisms can mistake it for a source of sulfur.
>
> I expect the bio-availability of Hg in pizza is pretty high
> considering how it bio-amplifies in fish, so I stand by my APE. But it
> is always prudent to read the MSDS before you open a bottle, and then
> read the MSDS of something similar just to put it in perspective.
>
> -James Holton
> MAD Scientist
>
> On 9/6/2017 12:59 PM, James Holton wrote:
>> Was just pointed out to me off-list that my anchovy data was off, so
>> I just double-checked the FDA website:
>>
>> https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644.htm
>>
>>
>> Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per
>> ounce (28g).
>>
>> So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the
>> Anchovie Pizza Equivalent.
>>
>> And it looks like one piece of bigeye tuna sushi could be as much as
>> ~14g*1.816ppm = 25 APEs
>>
>> -James Holton
>> MAD Scientist
>>
>> On 9/6/2017 11:44 AM, James Holton wrote:
>>> Something that could perhaps be of use here is what I like to call
>>> the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of
>>> mercury.  According to the Food and Drug Administration website here
>>> in the USA the average mercury content of anchovies is 0.34 ppm,
>>> which is about 1 microgram per ounce of fish.  Tuna can be higher,
>>> but varies a lot from fish to fish.  My point here is that most
>>> institutions regard the amount of mercury you bring onsite for
>>> purposes of eating for lunch, be it sushi or pizza, as small enough
>>> to be negligible.  I tend to agree.  So, one could argue that 1
>>> microgram of Hg per day is a "safe amount". Especially if you don't
>>> eat it.
>>>
>>> In terms of protein crystals, a 100 micron wide cube has a volume of
>>> 1 nanoliter, and if it were soaked to a final concentration of 50 mM
>>> Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng.  So, 100 protein
>>> crystals soaked with Hg add up to roughly 1 APE.  Please note that I
>>> am in no way encouraging you to eat your protein crystals, and
>>> especially not the solutions you soak them in.  You should do your
>>> own APE calculations for those.  But I do think it important to note
>>> just how tiny the amount of metal in our crystals really is.
>>>
>>> Now, mercury is purportedly the second-most-toxic metal after
>>> Plutonium.  But Pu derivatives are uncommon.  In fact, until
>>> recently (4zhd) Pu derivatives were unheard of. The authors I'm sure
>>> will tell you 4zhd involved no small amount of paperwork. But as

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

[Robbie Joosten]

Liquid mercury cannot be absorbed very well through the skin. Also ingestion 
seems to be much less risky than breathing in mercury vapours. My 
thermodynamics lecturer at uni was convinced that you can drink liquid mercury 
with no health risk, but I would not rec



Sent from my Windows 10 phone



From: George Sheldrick
Sent: 12 September 2017 20:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?



Over 50 years ago, a Toepler pump that I had glass-blown myself
developed a crack that caused several kilos of mercury to hit tha
ceiling and give me a shower. Fortunately I did not then know how
poisonous it was and suffered no ill-effects

George


On 12.09.2017 19:46, James Holton wrote:
> One more correction,
>
> It seems brominated vegetable oil (BMO) really does contain Br atoms!
> I could have sworn I read in some reputable source long ago that the
> process of "bromination" was an old term for general reduction of
> double bonds and did not necessarily involve bromine. Usually
> hydrogen.  I remembered this because I thought it was hugely
> counter-intuitive.  Now, of course, I cannot find that reference. So,
> who am I to pit the validity of my memory against Wikipedia and a long
> list of links to health-nut web blogs?  Guess I was wrong about that.
>
> The Mountain Dew I am drinking right now has a very faint X-ray
> fluorescence peak that could be Br.  Hard to be sure above
> background.  So I will have to get a sample of neat BMO to sit next to
> my shampoo, pepto and sunscreen on my shelf of heavy atom compounds
> that are on the FDA's GRAS list:
> https://www.fda.gov/food/ingredientspackaginglabeling/gras/
>
> Remarkably, the MSDS for BMO is less scary than that of ordinary
> vegetable oil.  This raises more than one interesting topic, but the
> most relevant here I think is "bio-availability". Selenomethionine is
> much much more bioavailable than selenium sulfide, which is the active
> ingredient in my dandruff shampoo. Apparently, humans don't absorb it,
> but microorganisms can mistake it for a source of sulfur.
>
> I expect the bio-availability of Hg in pizza is pretty high
> considering how it bio-amplifies in fish, so I stand by my APE. But it
> is always prudent to read the MSDS before you open a bottle, and then
> read the MSDS of something similar just to put it in perspective.
>
> -James Holton
> MAD Scientist
>
> On 9/6/2017 12:59 PM, James Holton wrote:
>> Was just pointed out to me off-list that my anchovy data was off, so
>> I just double-checked the FDA website:
>>
>> https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644.htm
>>
>>
>> Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per
>> ounce (28g).
>>
>> So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the
>> Anchovie Pizza Equivalent.
>>
>> And it looks like one piece of bigeye tuna sushi could be as much as
>> ~14g*1.816ppm = 25 APEs
>>
>> -James Holton
>> MAD Scientist
>>
>> On 9/6/2017 11:44 AM, James Holton wrote:
>>> Something that could perhaps be of use here is what I like to call
>>> the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of
>>> mercury.  According to the Food and Drug Administration website here
>>> in the USA the average mercury content of anchovies is 0.34 ppm,
>>> which is about 1 microgram per ounce of fish.  Tuna can be higher,
>>> but varies a lot from fish to fish.  My point here is that most
>>> institutions regard the amount of mercury you bring onsite for
>>> purposes of eating for lunch, be it sushi or pizza, as small enough
>>> to be negligible.  I tend to agree.  So, one could argue that 1
>>> microgram of Hg per day is a "safe amount". Especially if you don't
>>> eat it.
>>>
>>> In terms of protein crystals, a 100 micron wide cube has a volume of
>>> 1 nanoliter, and if it were soaked to a final concentration of 50 mM
>>> Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng.  So, 100 protein
>>> crystals soaked with Hg add up to roughly 1 APE.  Please note that I
>>> am in no way encouraging you to eat your protein crystals, and
>>> especially not the solutions you soak them in.  You should do your
>>> own APE calculations for those.  But I do think it important to note
>>> just how tiny the amount of metal in our crystals really is.
>>>
>>> Now, mercury is purportedly the second-most-toxic metal after
>>> Plutonium.  But Pu derivatives are uncommon.  In fact, until
>>> recently (4zhd) Pu derivatives were unheard of. The authors I'm sure
>>> will tell you 4zhd involved no small amount of paperwork. But as
>>> long as you are not working with Pu, you can regard every other
>>> metal as less toxic than Hg.
>>>
>>> Another good example is selenium; by far the most common metal
>>> derivative.  Although toxic, Se is also a dietary requirement. I
>>> suppose this is an excellent demonstration of what "moderation"

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

[Keller, Jacob]

Well, you can add to your list Silver sulfadiazine, mercurochrome, and 
merthiolate, all OTC antiseptics. The mercurochrome, since it contains Br, 
might be used as another standard for the Br edge.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Holton
Sent: Tuesday, September 12, 2017 1:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

One more correction,

It seems brominated vegetable oil (BMO) really does contain Br atoms!  I could 
have sworn I read in some reputable source long ago that the process of 
"bromination" was an old term for general reduction of double bonds and did not 
necessarily involve bromine. Usually hydrogen.  I remembered this because I 
thought it was hugely counter-intuitive.  Now, of course, I cannot find that 
reference. So, who am I to pit the validity of my memory against Wikipedia and 
a long list of links to health-nut web blogs?  Guess I was wrong about that.

The Mountain Dew I am drinking right now has a very faint X-ray fluorescence 
peak that could be Br.  Hard to be sure above background. So I will have to get 
a sample of neat BMO to sit next to my shampoo, pepto and sunscreen on my shelf 
of heavy atom compounds that are on the FDA's GRAS list:
https://www.fda.gov/food/ingredientspackaginglabeling/gras/

Remarkably, the MSDS for BMO is less scary than that of ordinary vegetable oil. 
 This raises more than one interesting topic, but the most relevant here I 
think is "bio-availability".  Selenomethionine is much much more bioavailable 
than selenium sulfide, which is the active ingredient in my dandruff shampoo.  
Apparently, humans don't absorb it, but microorganisms can mistake it for a 
source of sulfur.

I expect the bio-availability of Hg in pizza is pretty high considering how it 
bio-amplifies in fish, so I stand by my APE.  But it is always prudent to read 
the MSDS before you open a bottle, and then read the MSDS of something similar 
just to put it in perspective.

-James Holton
MAD Scientist

On 9/6/2017 12:59 PM, James Holton wrote:
> Was just pointed out to me off-list that my anchovy data was off, so I 
> just double-checked the FDA website:
>
> https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644
> .htm
>
>
> Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per 
> ounce (28g).
>
> So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the 
> Anchovie Pizza Equivalent.
>
> And it looks like one piece of bigeye tuna sushi could be as much as 
> ~14g*1.816ppm = 25 APEs
>
> -James Holton
> MAD Scientist
>
> On 9/6/2017 11:44 AM, James Holton wrote:
>> Something that could perhaps be of use here is what I like to call 
>> the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of 
>> mercury.  According to the Food and Drug Administration website here 
>> in the USA the average mercury content of anchovies is 0.34 ppm, 
>> which is about 1 microgram per ounce of fish.  Tuna can be higher, 
>> but varies a lot from fish to fish.  My point here is that most 
>> institutions regard the amount of mercury you bring onsite for 
>> purposes of eating for lunch, be it sushi or pizza, as small enough 
>> to be negligible.  I tend to agree.  So, one could argue that 1 
>> microgram of Hg per day is a "safe amount".  Especially if you don't 
>> eat it.
>>
>> In terms of protein crystals, a 100 micron wide cube has a volume of
>> 1 nanoliter, and if it were soaked to a final concentration of 50 mM 
>> Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng.  So, 100 protein 
>> crystals soaked with Hg add up to roughly 1 APE.  Please note that I 
>> am in no way encouraging you to eat your protein crystals, and 
>> especially not the solutions you soak them in.  You should do your 
>> own APE calculations for those.  But I do think it important to note 
>> just how tiny the amount of metal in our crystals really is.
>>
>> Now, mercury is purportedly the second-most-toxic metal after 
>> Plutonium.  But Pu derivatives are uncommon.  In fact, until recently
>> (4zhd) Pu derivatives were unheard of. The authors I'm sure will tell 
>> you 4zhd involved no small amount of paperwork. But as long as you 
>> are not working with Pu, you can regard every other metal as less 
>> toxic than Hg.
>>
>> Another good example is selenium; by far the most common metal 
>> derivative.  Although toxic, Se is also a dietary requirement. I 
>> suppose this is an excellent demonstration of what "moderation"
>> really means.  The Recommended Daily Allowance (RDA) of selenium in 
>> the USA for adult men and pregnant women is 55-60 micrograms per day.  
>> In crystals, one Se atom per 100 amino acids at 50% solvent comes to 
>> an overall concentration of 50 mM.  So, a 100 micron crystal contains 
>> about 4 ng of Se.  It would take 15,000 such crystals to add up to 
>> the US RDA.  The synchrotrons I work at don't go 

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

[George Sheldrick]

Over 50 years ago, a Toepler pump that I had glass-blown myself 
developed a crack that caused several kilos of mercury to hit tha 
ceiling and give me a shower. Fortunately I did not then know how 
poisonous it was and suffered no ill-effects


George


On 12.09.2017 19:46, James Holton wrote:

One more correction,

It seems brominated vegetable oil (BMO) really does contain Br atoms!  
I could have sworn I read in some reputable source long ago that the 
process of "bromination" was an old term for general reduction of 
double bonds and did not necessarily involve bromine. Usually 
hydrogen.  I remembered this because I thought it was hugely 
counter-intuitive.  Now, of course, I cannot find that reference. So, 
who am I to pit the validity of my memory against Wikipedia and a long 
list of links to health-nut web blogs?  Guess I was wrong about that.


The Mountain Dew I am drinking right now has a very faint X-ray 
fluorescence peak that could be Br.  Hard to be sure above 
background.  So I will have to get a sample of neat BMO to sit next to 
my shampoo, pepto and sunscreen on my shelf of heavy atom compounds 
that are on the FDA's GRAS list:

https://www.fda.gov/food/ingredientspackaginglabeling/gras/

Remarkably, the MSDS for BMO is less scary than that of ordinary 
vegetable oil.  This raises more than one interesting topic, but the 
most relevant here I think is "bio-availability". Selenomethionine is 
much much more bioavailable than selenium sulfide, which is the active 
ingredient in my dandruff shampoo. Apparently, humans don't absorb it, 
but microorganisms can mistake it for a source of sulfur.


I expect the bio-availability of Hg in pizza is pretty high 
considering how it bio-amplifies in fish, so I stand by my APE. But it 
is always prudent to read the MSDS before you open a bottle, and then 
read the MSDS of something similar just to put it in perspective.


-James Holton
MAD Scientist

On 9/6/2017 12:59 PM, James Holton wrote:
Was just pointed out to me off-list that my anchovy data was off, so 
I just double-checked the FDA website:


https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644.htm 



Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per 
ounce (28g).


So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the 
Anchovie Pizza Equivalent.


And it looks like one piece of bigeye tuna sushi could be as much as 
~14g*1.816ppm = 25 APEs


-James Holton
MAD Scientist

On 9/6/2017 11:44 AM, James Holton wrote:
Something that could perhaps be of use here is what I like to call 
the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of 
mercury.  According to the Food and Drug Administration website here 
in the USA the average mercury content of anchovies is 0.34 ppm, 
which is about 1 microgram per ounce of fish.  Tuna can be higher, 
but varies a lot from fish to fish.  My point here is that most 
institutions regard the amount of mercury you bring onsite for 
purposes of eating for lunch, be it sushi or pizza, as small enough 
to be negligible.  I tend to agree.  So, one could argue that 1 
microgram of Hg per day is a "safe amount". Especially if you don't 
eat it.


In terms of protein crystals, a 100 micron wide cube has a volume of 
1 nanoliter, and if it were soaked to a final concentration of 50 mM 
Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng.  So, 100 protein 
crystals soaked with Hg add up to roughly 1 APE.  Please note that I 
am in no way encouraging you to eat your protein crystals, and 
especially not the solutions you soak them in.  You should do your 
own APE calculations for those.  But I do think it important to note 
just how tiny the amount of metal in our crystals really is.


Now, mercury is purportedly the second-most-toxic metal after 
Plutonium.  But Pu derivatives are uncommon.  In fact, until 
recently (4zhd) Pu derivatives were unheard of. The authors I'm sure 
will tell you 4zhd involved no small amount of paperwork. But as 
long as you are not working with Pu, you can regard every other 
metal as less toxic than Hg.


Another good example is selenium; by far the most common metal 
derivative.  Although toxic, Se is also a dietary requirement. I 
suppose this is an excellent demonstration of what "moderation" 
really means.  The Recommended Daily Allowance (RDA) of selenium in 
the USA for adult men and pregnant women is 55-60 micrograms per 
day.  In crystals, one Se atom per 100 amino acids at 50% solvent 
comes to an overall concentration of 50 mM.  So, a 100 micron 
crystal contains about 4 ng of Se.  It would take 15,000 such 
crystals to add up to the US RDA.  The synchrotrons I work at don't 
go thought that many crystals every day.  But even if they did, I'd 
stick to my commercially available multivitamin to get my dietary 
selenium.


So, although it is never a good idea to be sloppy with chemicals in 
the lab, I think it is also important to do the math and think about 
not 

[ccp4bb] Macromolecular Crystallography workshop in South America

[Felipe]

Dear colleagues,

We are pleased to announce our sixth edition of the Workshop:

Macromolecular Crystallography School "From data processing to structure 
refinement and beyond", to be held at the Institut Pasteur de Montevideo 
(Uruguay).

This Workshop will cover all aspects of the macromolecular structure 
determination process using X ray crystallography: starting from data 
processing, through phasing and refinement to structure completion and 
analysis. Integrative methods are also being included. In particular, this year 
an introduction to  cryo-electron microscopy has been added to the program.

http://pasteur.uy/mx2017 

Dates: November 13 - 23, 2017

Confirmed speakers and tutors:

Alejandro Buschiazzo, Montevideo, Uruguay
Grzegorz Chojnowski, Hamburg, Germany
Paul Emsley, Cambridge, UK
Richard Garrat, São Carlos, Brazil
James Holton, San Francisco/Berkeley/Palo Alto, USA
Ronan Keegan, Oxford, UK
Eugene Krissinel, Oxford, UK
Andrey Lebedev, Oxford, UK
Andrew Leslie, Cambridge, UK
Garib Murshudov, Cambridge, UK
Colin Palmer, Oxford, UK
James Parkhurst, Oxford, UK
Randy Read, Cambridge, UK
Clemens Vonrhein, Cambridge, UK


Please find the program of the Workshop, the application form and further 
contact information, at http://pasteur.uy/mx2017 

This Workshop is supported by the Collaborative Computational Project Nº4 
(CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de 
Biologia Estructural del Mercosur (CeBEM); the International Union of 
Crystallography (IUCr); and the Institut Pasteur de Montevideo.

Organizers:
Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom
Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil

Applicants:
24 students will be selected, aiming at advanced PhD, postdocs and young 
researchers. The Course will provide financial support covering registration 
fees, and for the case of those students coming from abroad, all local expenses 
(lodging, per diem and local transportation). Look in the www site for details 
on application procedures.

The application deadline is September 17, 2017.

Please address further inquiries to: mx2...@pasteur.edu.uy 


Looking forward to welcoming you in Montevideo!

Felipe Trajtenberg, PhD
Laboratory of Molecular & Structural Microbiology
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +598 25220910 int. 143
Fax:  +598 25224185
http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular-eng

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

[James Holton]

One more correction,

It seems brominated vegetable oil (BMO) really does contain Br atoms!  I 
could have sworn I read in some reputable source long ago that the 
process of "bromination" was an old term for general reduction of double 
bonds and did not necessarily involve bromine. Usually hydrogen.  I 
remembered this because I thought it was hugely counter-intuitive.  Now, 
of course, I cannot find that reference. So, who am I to pit the 
validity of my memory against Wikipedia and a long list of links to 
health-nut web blogs?  Guess I was wrong about that.


The Mountain Dew I am drinking right now has a very faint X-ray 
fluorescence peak that could be Br.  Hard to be sure above background.  
So I will have to get a sample of neat BMO to sit next to my shampoo, 
pepto and sunscreen on my shelf of heavy atom compounds that are on the 
FDA's GRAS list:

https://www.fda.gov/food/ingredientspackaginglabeling/gras/

Remarkably, the MSDS for BMO is less scary than that of ordinary 
vegetable oil.  This raises more than one interesting topic, but the 
most relevant here I think is "bio-availability".  Selenomethionine is 
much much more bioavailable than selenium sulfide, which is the active 
ingredient in my dandruff shampoo.  Apparently, humans don't absorb it, 
but microorganisms can mistake it for a source of sulfur.


I expect the bio-availability of Hg in pizza is pretty high considering 
how it bio-amplifies in fish, so I stand by my APE.  But it is always 
prudent to read the MSDS before you open a bottle, and then read the 
MSDS of something similar just to put it in perspective.


-James Holton
MAD Scientist

On 9/6/2017 12:59 PM, James Holton wrote:
Was just pointed out to me off-list that my anchovy data was off, so I 
just double-checked the FDA website:


https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644.htm 



Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per 
ounce (28g).


So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the 
Anchovie Pizza Equivalent.


And it looks like one piece of bigeye tuna sushi could be as much as 
~14g*1.816ppm = 25 APEs


-James Holton
MAD Scientist

On 9/6/2017 11:44 AM, James Holton wrote:
Something that could perhaps be of use here is what I like to call 
the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of 
mercury.  According to the Food and Drug Administration website here 
in the USA the average mercury content of anchovies is 0.34 ppm, 
which is about 1 microgram per ounce of fish.  Tuna can be higher, 
but varies a lot from fish to fish.  My point here is that most 
institutions regard the amount of mercury you bring onsite for 
purposes of eating for lunch, be it sushi or pizza, as small enough 
to be negligible.  I tend to agree.  So, one could argue that 1 
microgram of Hg per day is a "safe amount".  Especially if you don't 
eat it.


In terms of protein crystals, a 100 micron wide cube has a volume of 
1 nanoliter, and if it were soaked to a final concentration of 50 mM 
Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng.  So, 100 protein 
crystals soaked with Hg add up to roughly 1 APE.  Please note that I 
am in no way encouraging you to eat your protein crystals, and 
especially not the solutions you soak them in.  You should do your 
own APE calculations for those.  But I do think it important to note 
just how tiny the amount of metal in our crystals really is.


Now, mercury is purportedly the second-most-toxic metal after 
Plutonium.  But Pu derivatives are uncommon.  In fact, until recently 
(4zhd) Pu derivatives were unheard of. The authors I'm sure will tell 
you 4zhd involved no small amount of paperwork. But as long as you 
are not working with Pu, you can regard every other metal as less 
toxic than Hg.


Another good example is selenium; by far the most common metal 
derivative.  Although toxic, Se is also a dietary requirement. I 
suppose this is an excellent demonstration of what "moderation" 
really means.  The Recommended Daily Allowance (RDA) of selenium in 
the USA for adult men and pregnant women is 55-60 micrograms per 
day.  In crystals, one Se atom per 100 amino acids at 50% solvent 
comes to an overall concentration of 50 mM.  So, a 100 micron crystal 
contains about 4 ng of Se.  It would take 15,000 such crystals to add 
up to the US RDA.  The synchrotrons I work at don't go thought that 
many crystals every day.  But even if they did, I'd stick to my 
commercially available multivitamin to get my dietary selenium.


So, although it is never a good idea to be sloppy with chemicals in 
the lab, I think it is also important to do the math and think about 
not just the toxicity of the things we work with on the bench, but 
the everyday items all around us.  It is never a good idea to be 
antagonistic with regulators about such things. They are only trying 
to do their job, and all they are trained to know about are LD50s and 
how to stay as far below 

[ccp4bb] Protein Crystallography web course at Birkbeck College

[Tracey Barrett]

Dear all,
registration is currently open for the postgraduate certificate 
course in Protein Crystallography via the web at Birkbeck that begins on 
Monday, October the 2nd. It is for the duration of 1 year during which all 
aspects of protein crystallography will be covered from the fundamentals 
of protein structure to model validation. The emphasis is very much on 
techniques and the underlying principles so is ideally suited to students 
currently enroled on PhD programs or those who wish to expand their skills 
in structural biology. Information on registration and course content can 
be found at: http://px17.cryst.bbk.ac.uk/px/course/course.htm under 
"General course information" or contact Tracey Barrett at 
p...@mail.cryst.bbk.ac.uk for further details.


Although a stand-alone course, the postgraduate certificate in protein 
crystallography can also be taken as part of the MSc in Structural 
Molecular Biology. For more details, please see 
http://www.bbk.ac.uk/study/2017/postgraduate/programmes/TMSBISCL_C/


Best wishes,

Tracey



Dr Tracey Barrett,
Crystallography,
Senior Lecturer in Structural Biology,
Institute for Structural and Molecular Biology,
Birkbeck College,
Malet Street,
London WC1E 7HX
Tel: 020 7631 6822
Fax: 020 7631 6803