P212121

The context is always important, but this should give you a fighting chance at giving a meaningful response instead of a blank stare (if you want). Please note, this list is noninclusive.

1) ‘having trouble with the PCR’
meaning: rough start since it is nearly the first step a crystallographer does
response: oh, don’t worry it will work eventually

2) ‘having trouble with express’
meaning: the bacteria (or yeast etc..) are not producing their desired protein
response: bummer, what have you tried so far? (you can space out as they list things) then respond with ‘wow, can’t believe it hasn’t worked yet’

3) ‘I can’t get my protein out of the pellet’
meaning: once the cells have be lysed and centrifuged at a high speed their desired protein is no longer in solution
response: Have you tried lysing the pellet?

4) ‘I keep losing my protein’
meaning: this will happen during purification or using concentrators
response: Have you tried using a different concentrator? (virtually, no one does)

5) ‘precipitates out of solution’
meaning: the protein comes out of solution and can end up looking like dandruff
response: Have you tried finding another buffer for you protein?

6) ‘We only got (number greater than 4) angstrom diffraction’
meaning: the diffraction is not good
response: Do you have any more crystals?

7) ‘have a high mosaic spread’
meaning: the crystal is not well ordered
response: Do you have any more crystals?

‘not getting any hits when I set up expansions’
meaning: a hit is a solution (condition) that may yields a protein crystal
response: Strange.

9) ‘for some reason it won’t index’
meaning: just started data processing and trying to determine the space group
response: Are you sure the beam center is correct?

10) ‘the map doesn’t look right’
meaning: data processing is not going well
response: Hmm, are you sure the space group is right?

Kissing waters: two blobs of electron density that are linked.

Ideally, the kissing waters will end up being your ligand of interest.

If your research involves immunoglobulins, T cell receptors, major histocompatibility complex or related proteins of the immune system then the IMGT/3Dstructure-DB is worth checking out.

I am a fan of making the PDB more useful and this database fits the bill.

This database helps to reduce performing sequence alignments by displaying amino acid sequences from specific regions. If you have worked with the Kabat books then you will certainly appreciate this resource.

Here is an abbreviated search example containing the CDR3s of various immunoglobulins:


Also the database will allow you to search by receptor type, protein name, species and more.

The FAQ on the IMGT/3Dstructure-DB is quite good because it explains the terms used in their database, not just how the database functions. This allows a non-expert in the field to use and understand what is going on, thus making their database an even better resource.