Multi-contoured electron Density maps

December 4, 2015

When wandering around the department, I am struck by how few crystallographers use multiple contoured electron density maps* whilst building. I really don’t understand this: YOU’RE THROWING AWAY INFORMATION PEOPLE!

Even at moderate resolution, the information gained can be invaluable:

  1. Precisely locating a heavy atom in a big blob of electron density. The Atom will sit at the highest point of the map. IF you are using multiple contours, this will be obvious! (figure 1)
  2. Resolving His/Asn/Gln sidechain flips. A bit more prone to noise here – but in terms of electrons, O > N > C. You can easily decide which way around Asn and Gln side chains should point, and often get some help with His side chains as well. (figure 2)
Screenshot 2015-12-04 13.05.44

Figure 1a: THAR SHE BLOWS!

This calcium ion sits RIGHT on the peak in the electron density map. No ambiguity where it lies. A single map contoured at 1 sigma is not helpful.

Screenshot 2015-12-04 13.07.38

Figure 1b: Nope. Not helpful.

 

Screenshot 2015-12-04 12.54.32

Figure 2: Gln sidechain flips, made easy…

The increased electron density  on the right hand side here indicate that this Gln residue is the correct way around. Again, a single map contoured at 1 sigma is no use here.

I realise that there are other ways to achieve what I have described, but when you are building your models, saving time and making things easier is hugely helpful. I find using multi-contouring incredibly helpful.

* multi-contours shown here are made using the “Multi-chicken” command in COOT (extensions>maps>multi-chicken). Multi-chicken creates 10 maps contoured at 1,1.5,2, 2.5, etc sigma. I find the default setting is a tad dark so I use “brighten maps” (extensions>maps>brighten maps) a couple of times to sort that out. I then contour the original map at 0.7sigma (depending upon noise) and make it really deep purple.

All screenshots made with COOT.

 

Advertisements

E.coli can make Disulphide bonds if you ask it nicely.

May 25, 2012

Human protein, expressed in NEB SHuffle cells, correctly folded, crystallised, solved, etc.


Electron density around a Disulphide bond – which E.coli cannot make in their cytoplasm normally – unless you tinker with a few genes here and there.

The Disulphide is the bond between the two green sulphur atoms in the centre of the image

EDIT: Click to see the picture more clearly – I don’t know what WP has done to it, but it should look crisper than that.