On 01/26/2020 01:02 PM, benjamin bax wrote:
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Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
to produce the crystal.
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/pdbx_exptl_crystal_grow_comp.html
<https://urldefense.proofpoint.com/v2/url?u=http-3A__mmcif.wwpdb.org_dictionaries_mmcif-5Fpdbx-5Fv40.dic_Categories_pdbx-5Fexptl-5Fcrystal-5Fgrow-5Fcomp.html&d=DwMFAg&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=tFmtHzRSYSNKNBOBWtxsEO40zWcLoOkoIXetemSX_Ww&s=sd6UCKtr0m8elxTeVn-b2s-NtJt48C2HFTcUsXtq2NQ&e=>
loop_
_pdbx_exptl_crystal_grow_comp.crystal_id
_pdbx_exptl_crystal_grow_comp.sol_id
_pdbx_exptl_crystal_grow_comp.comp_id
_pdbx_exptl_crystal_grow_comp.comp_name
_pdbx_exptl_crystal_grow_comp.conc
_pdbx_exptl_crystal_grow_comp.conc_range
_pdbx_exptl_crystal_grow_comp.conc_units
4 'protein' 1 'protein' 25. . 'mg/ml'
4 'protein' 2 'Tris HCl' 20. . 'millimolar'
4 'protein' 3 'NaCl' 0.2 . 'molar'
4 'precipitant' 1 'PEG 4000' 12.5 . 'percent_weight_by_volume'
4 'precipitant' 2 'MES' 0.1 . 'molar'
pdbout copy remarks 280
One argument against PDBX_EXPTL_CRYSTAL_GROW_COM is that it perpetuates (at least in this example) the
incorrect/deprecated use of "%w/v". This is a measure of the mass concentration of the component,
exactly the same as g/L or mg/ml. There is no reason to use different units for the same measure for
different components. The valid use of % is when all components will add up to 100%, which is not the case
for %w/v. Sigma used to sell a 1 g/ml solution of TCA in water as "100% w/v TCA". I wonder, how
many people thought 100% meant pure TCA? Wikipedia is not authoritative, but the logic of the following (from
article on "Volume Fraction") is compelling:
Terminology
'"Percent concentration" does not refer to this quantity. This improper name persists, especially in elementary textbooks. In
biology, the unit "%" is sometimes (incorrectly) used to denote mass concentration, also called "mass/volume
percentage." A solution with 1 g of solute dissolved in a final volume of 100 mL of solution would be labeled as "1 %" or
"1 % m/v" (mass/volume). This is incorrect because the unit "%" can only be used for dimensionless quantities. Instead,
the concentration should simply be given in units of g/mL.'
We all know that a 1% w/v solution contains 1 g of the component in question,
per 100 ml of solution. It does not mean that that component makes up 1% of the
mass of the solution, or 1% of the volume. It does not give us any better
intuition into the amount of the compound present than would 1 g/100 ml or 10
g/L. In fact it interferes with intuition, if other components are given in
mg/ml. In the example above, is the amount of PEG more or less than the amount
of protein (by weight)? 12.5% peg is 125 mg/ml, so 5-fold excess over protein
by weight. Suppose you are told that for a general rule when dissolving
biological membranes with low-CMC detergents, start off with 1:1 ratio of
protein:detergent. You want to solubilize your protein at 15 g/L. What should
the detergent concentration be? Also 15 g/l, but the stock bottle is labeled
20% w/v. You either convert 15 g/L to 1.5% or convert 20% to 200 g/L before you
can calculate the volume to add. Not very hard, but for what??
Happy Lunar New Year,
eab
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