[ccp4bb] Vapor diffusion calculator

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: DLS
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2010-02-04

Next message:
Subject: Dynamics Software for DynaPro DLS?
From: Melanie Adams-Cioaba maa23 {- at -} PSU {- dot -} EDU
Date: 2010-02-04

Subject: Vapor diffusion calculator
From: Patrick Shaw Stewart Patrick {- at -} DOUGLAS {- dot -} CO {- dot -} UK
Date: 2010-02-04

Jacob and CCP4bb

It's not exactly what you're looking for, but my colleague Peter Baldock
wrote a program called "VD to MB" a few years ago that does part of the
job. It was a program to convert vapor diffusion crystallization
conditions into microbatch-under-oil conditions.

I tried it back then with several published and unpublished examples
where crystallization had been optimized in both vapor diffusion and
microbatch. I was originally sceptical, but it seemed to work
remarkably well, generally getting the numbers right to within 5 or 10%.

The program uses a parameter called "1/e equilibration time for 1M salt
(days)". I originally used a value of 1, but I think we changed it to
0.5 for 96-well plates. Obviously the value will depend on the geometry
of the plates. Does anyone have any practical information about
equilibration times?

Different salts have very different effects on vapor pressure. I found
a list in an old "Rubber Book" (CRC Handbook of Physics and Chemistry)
part of which I have pasted below. I tried quite hard to make sense of
this list - hoping that it would also shed light on the
protein-precipitating effect of salts - but concluded that the numbers
are pretty random apart from obvious valence effects. (Someone here may
be able to explain them, though!)

You can download the program from http://www.douglas.co.uk/tipsntech.htm
near the middle of the page. There's also an equivalent Excel
spreadsheet for playing around with.

See also http://www.douglas.co.uk/convert.htm for some (very old but
still valid!) examples and comments.

Also bear in mind that - with many proteins - roughly half of the
protein is lost on the surface of VD drops for 100 + 100 nl drops.

Peter also wrote an algorithm - now in our optimization software - that
calculates the pH of a solution with any number of buffers in it, where
the buffers can be at different concentrations too. A sort of super
Henderson-Hasselbalch. If anyone is interested I'm sure Peter could
show you the maths or pass on the code (it took him about a month of
lunch-breaks!)

Best wishes

Patrick

_____________________________

Reduction of vapor pressure in mmHg due to the presence of 1M salt at
100C

(at which temperature the vapor pressure of water is 760 mmHg)

From Handbook of Physics and Chemistry, 76th Ed

CdSO4

8.9

ZnSO4

10.4

MnSO4

10.5

FeSO4

10.7

MgSO4

12

CdI2

14.8

CdBr2

17.8

ZnCl2

18.7

CdCl2

18.8

KNO3

21.1

NH4NO3

22

NaNO3

22.5

NH4Cl

23.7

NH4Br

23.9

NH42SO4

24

KCl

24.4

Na2SO4

25

NaCl

25.2

KI

25.3

LiCl

25.5

LiNO3

25.9

NaBr

25.9

LiBr

26.2

BaNO32

27

Li2SO4

28.1

LiI

28.6

K2CrO4

29.5

Na3PO4

30

Li2CrO4

32.6

MnCl2

34

CaNO32

34.8

CoCl2

34.8

Al2S043

36.5

BaCl2

36.7

NiCl2

37

NiNO32

37.3

BaBr2

38.8

MgCl2

39

CaCl2

39.8

MgNO32

42

MgBr2

44

CaBr2

44.2

AlCl3

61

StDev

10.7

Av

27.7

CV

0.4

--

For information and discussion about protein crystallization and
automation, please join

our bulletin board at
http://groups-beta.google.com/group/oryx_group?hl=en

patrick@douglas.co.uk Douglas Instruments Ltd.

DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK

Directors: Peter Baldock, Patrick Shaw Stewart

http://www.douglas.co.uk/

Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034

Regd. England 2177994, VAT Reg. GB 480 7371 36

> -----Original Message-----

> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of

> Jacob Keller

> Sent: 02 February 2010 22:34

> To: CCP4BB@JISCMAIL.AC.UK

> Subject: [ccp4bb] Vapor diffusion calculator

>

> Dear Crystallographers,

>

> Is anybody aware of a calculator for vapor diffusion experiments to

> plot

> concentrations of various solvent components as a function of time?
For

> a

> simple example, what happens when I mix a protein solution containing

> 50mM

> NaCl 1:1 with a reservoir containing 50% MPD but no salt? Where is the

> vapor

> diffusion equilibrium, and how does the drop composition change as a

> function of time? More complicated would be experiments involving

> volatile

> components other than water, as I think, for example, ethanol would

> almost

> instantly equilibrate, then the water diffusion would kick in over a

> longer

> time scale. Even more complicated would be pH-dependent volatilities

> such as

> acetate. I don't think this would be impossible to figure out, but it

> would

> be nice if there were a pre-existing tool/server to do such.

>

> Regards,

>

> Jacob Keller

>

>

> *******************************************

> Jacob Pearson Keller

> Northwestern University

> Medical Scientist Training Program

> Dallos Laboratory

> F. Searle 1-240

> 2240 Campus Drive

> Evanston IL 60208

> lab: 847.491.2438

> cel: 773.608.9185

> email: j-keller2@northwestern.edu

> *******************************************

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: DLS
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2010-02-04

Next message:
Subject: Dynamics Software for DynaPro DLS?
From: Melanie Adams-Cioaba maa23 {- at -} PSU {- dot -} EDU
Date: 2010-02-04