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Contents

Top 14 organic and inorganic main precipitants reported in REMARK 280 of the PDB
(from the 3939 entries that could be parsed.)
           
Organic precipitant
(2503 samples)
No. of entries Average conc. used   Salt precipitant
(1436 samples)
No. of entries Average conc. used
 PEG 4K 710 21.1%    Ammonium sulfate 900 1.9 M
 PEG 8K 488 18.1%    Sodium chloride 124 1.7 M
 PEG 3.35K 296 20.5%    Sodium citrate 76 1.1 M
 PEG 6K 212 16.8%    Sodium, potassium phos. 66 1.8 M
 MPD 193 38.6%    Lithium sulfate 63 1.4 M
 PEG 400 142 25.7%    Sodium formate 59 3.4 M
 PEG-MME 2000 65 22.7%    Magnesium sulfate 29 1.7 M
 PEG-MME 5000 63 20.0%    Ammonium phosphate 29 1.5 M
 PEG 1000 57 19.8%    Potassium phosphate 25 2.0 M
 Iso-propanol 48 18.0%    Sodium acetate 21 1.2 M
 PEG 2000 45 22.3%    Sodium, potassium tart. 13 1.0 M
 Ethylene glycol 43 20.5%    Cesium chloride 11 2.7 M
 Ethanol 43 28.8%    Potassium chloride 10 1.4 M
 PEG 10K 32 22.0%    Sodium phosphate 10 1.4 M
Total, average 2437 22.5%    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:

  1. 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.
  2. 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. 
  3. Millimolar units (MM) were converted to molar (M) units.
  4. In cases where REMARK 280 only mentioned salts, the salt with the highest molarity was considered to be the main precipitant.
  5. 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.
  6. 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.
  7. 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.)
  8. 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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