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Top 14 organic and inorganic main precipitants reported in REMARK 280 of
the PDB |
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(from the 3939 entries that could be parsed.) |
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Organic precipitant
(2503 samples) |
No. of entries |
Average conc. used |
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Salt precipitant
(1436 samples) |
No. of entries |
Average conc. used |
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PEG 4K |
710 |
21.1% |
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Ammonium sulfate |
900 |
1.9 M |
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PEG 8K |
488 |
18.1% |
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Sodium chloride |
124 |
1.7 M |
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PEG 3.35K |
296 |
20.5% |
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Sodium citrate |
76 |
1.1 M |
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PEG 6K |
212 |
16.8% |
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Sodium, potassium phos. |
66 |
1.8 M |
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MPD |
193 |
38.6% |
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Lithium sulfate |
63 |
1.4 M |
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PEG 400 |
142 |
25.7% |
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Sodium formate |
59 |
3.4 M |
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PEG-MME 2000 |
65 |
22.7% |
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Magnesium sulfate |
29 |
1.7 M |
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PEG-MME 5000 |
63 |
20.0% |
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Ammonium phosphate |
29 |
1.5 M |
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PEG 1000 |
57 |
19.8% |
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Potassium phosphate |
25 |
2.0 M |
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Iso-propanol |
48 |
18.0% |
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Sodium acetate |
21 |
1.2 M |
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PEG 2000 |
45 |
22.3% |
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Sodium, potassium tart. |
13 |
1.0 M |
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Ethylene glycol |
43 |
20.5% |
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Cesium chloride |
11 |
2.7 M |
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Ethanol |
43 |
28.8% |
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Potassium chloride |
10 |
1.4 M |
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PEG 10K |
32 |
22.0% |
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Sodium phosphate |
10 |
1.4 M |
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Total, average |
2437 |
22.5% |
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Total, average |
1436 |
1.7 M |
Ammonium sulfate was the most popular with 900 entries,
followed by PEG 4K and PEG 8K. However, if you combine the medium and high
molecular-weight PEGs (1968 entries) they easily outnumber ammonium sulfate.
Salts are generally less popular than organic materials.
Notes:
- These data were extracted from REMARK 280 using the
complete set of PDB files around January 2005. Roughly 4800 conditions
could be extracted with the names of ingredients and the concentrations used.
- In cases where the concentration of the salt was measured
in % (presumed to be the percentage of the saturated solution) the concentration was
converted to molar units, or in some cases the condition was not used.
- Millimolar units (MM) were converted to molar (M) units.
- In cases where REMARK 280 only mentioned salts, the salt with the highest molarity was
considered to be the main
precipitant.
- In cases which included only organic materials, the
organic material with the highest concentration (whether %, %w/v or %v/v etc.)
was considered to be the main precipitant.
- In cases where both salts and organics were
mentioned, the following procedure was adopted to determine which was the main
precipitant: the highest percentage (%w/v or %v/v) of organic precipitant in a
condition was compared with the highest molarity (M) of salt.
If the salt molarity was greater than the percentage of organic material divided
by 10, the precipitant was considered to be the salt. If less, the organic
material. If these two numbers were within 0.2 of each other, the condition was
excluded. As a
hypothetical example, if a condition contained 6% PEG 4000 and 0.9 M Ammonium sulfate, the salt would be considered the main precipitant. This
rough-and-ready procedure seemed to agree with intuition.
- Conditions were excluded where glycerol came out as the "main precipitant", since this material is not a precipitant - indeed it
often increases the solubility of a protein. (Many of these conditions
appeared to be low ionic strength "salting in" conditions.)
- Peat et al. published a similar list of chemicals in "Tapping the
Protein Data Bank for crystallization conditions", Acta Cryst. D61 (2005),
pp1662-1669. This list is broadly in agreement with the above table.
However, there are differences because Peat et al. included all
ingredients (including buffers, additives etc.) without attempting to judge
which was the main precipitant.
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