What is the NKI set?

The NKI set is a dual screen set which was first routinely used by the Netherlands Cancer Institute (Het Nederlands Kanker Instituut), hence the name. A breakdown of the conditions is available on the C6 website. It combines the diversity of a sparse matrix set up with the logic of a systematic layout. For many years this was our default set up if you’ve no idea about where to start, but it has been  recently replaced with Shotgun and PACT.

How was it developed?

“…The sparse-matrix screen is the cherry-picked combination of conditions from the Joint Center for Structural Genomics (JCSG) extended using conditions from other screens. Its aim is to maximize the coverage of crystallization parameter space with no redundancy. The systematic screen, a pH, anion and cation testing (PACT) screen, aims to decouple the components of each condition and to provide information about the protein, even in the absence of crystals, rather than cover a wide crystallization space…” (Extracted from: Towards rationalization of crystallization screening for small to medium-sized academic laboratories, Newman et al, Acta Cryst. (2005) D61, 1426–1431).

A picture is worth 1000 words:

Below are pH assays, JSCG+ on top and PACT on the bottom. JCSG+ has a range of randomly arrayed pH values, which is in line with the sparse matrix set up. PACT on the other hand shows beautiful arrangement of pH values in each of the quadrants of the layout, and this makes it incredibly easy to figure out if your protein ‘likes’ a certain pH and chemical condition.

JCSG+ pH plate: it is immediately apparent that there is a wide diversity of pH spread over the plate (red is acidic -> yellow -> green -> blue is basic)

PACT pH plate: you can see the trend in pH in each of the quadrants (red is acidic -> yellow -> green -> blue is basic)