Princeton University   |   Department of Molecular Biology

Recently Published Structures
Telomere G-quadruplex
with mesoporphyrin

Structure determinations fall into two classes: those with homology to existing structures in PDB; those with novel structures or with low sequence identity to any known structure.

You can get a quick indication of how homologous your molecule is to an existing structure by using a BLAST protein search and selecting the "Protein Data Bank" as the sequence database. If you find extended matches with greater than 40% sequence identity, you have decent odds of solving your structure by the method of molecular replacement. A single good data set can suffice to determine the structure. Most structures uploaded to PDB are now solved by this method. The method also gives a reasonable starting model to iteratively rebuild and refine the model toward the one respresenting your structure. A recent example of a structure determined by molecular replacement using the facility's resources is the Vps33:Vps16 subcomplex from HOPS. We prefer the programs Phaser and Molrep for most of our work but have also used Phenix.Rosetta for a recent difficult structure determination of the Rap phosphatase RapI - an external collaboration with Prof. Matthew Neiditch at Rutgers.

Sec12 experimentally-phased electron density map
from SelenoMethionine MAD data collected at the synchrotron

If you've got a novel structure with no viable homologs, then we end up using multiple crystals and multiple data sets to determine the structure by an experimental phasing method. Most of the time this is via SelenoMethionine-enriched protein using the single- or multiwavelength anomalous diffraction methods (SAD and MAD) from the selenium atom signal at that element's absorption edge. We can also use SAD or MAD techniques with proteins soaked in heavy metal compounds (Pt, Au, Hg, Sm, Au etc). Depending on nature of the problem this often yields phased data that is straightforward to interpret - and perhaps even amenable to auto-building using powerful modern software like Arp/wArp or Phenix. At other times it requires significant manual building leveraging both cutting edge crystallographic programs and the experience of building nearly a hundred such structures to finish up a structure. Either way, we've got 25 years experience tackling problems of this nature, small and large. The gallery at the top of this page represents a small subset of over 25 protein structure publications produced with facility resources in the last decade alone. Recent examples of structures solved using experimental phasing include the Vps33 monomer structure from HOPS, and the Sec12 guanine exchange factor from Saccharomyces cerevisiae. We used the experimentally-phased Vps33 structure to solve the Vps33:Vps16 structure by molecular replacement.


Modern computers have got to the point where it's no longer necessary to drop $75,000 on a Silicon Graphics workstation to solve crystal structures. You can do structures on your MacBook, although not on your iPad. Silicon Graphics no longer even exists as a company. We can help you install and configure your own crystallographic software suite if you wish, if you choose to go this route rather than use one of the facility computers.

Linux and Mac OSX are the easiest options because they are both based on Unix operating systems which match the development environments for most of the useful software packages. If you're running Windows consider using a virtual machine to run Linux as your main crystallographic environment. We highly recommend CCP4, a comprehensive and mature software suite developed by academics for x-ray crystallography. CCP4 incorporates the Coot project, which is the graphical program we strongly recommend to manipulate your structure with. We also recommend Phenix which is an ever-expanding set of programs that while buggier than CCP4 often has more bleeding-edge methods (for better or for worse).

A [CCP4 + Coot + Phenix] installation should give you a fairly full-featured range of programs to solve and build structures with.