Even if crystal data is given, PISA provides analysis of oligomeric states as if it was not, in addition to the "proper" analysis. The corresponding results are found in the "No crystal" tab of the Control Panel.

1. There are natural limits for any computational procedure to match experimental observations, specifically in PISA:
    
   1. approximations in theoretical models describing macromolecular interactions.
   2. imperfect calibration of empirical and semiempirical parameters
   3. using the concept of "average conditions", where complexes are detected, with unspecified pH, salinity, ionic strength, presence of other solutes and other factors. "Average conditions" are implicitely hardcoded in a set of calibrated parameters of macromolecular interactions, used by PISA, and they cannot be good in all cases.
 

2. There could also be reasons on the experimental side:
    
   1. poor resolution or refinement. PISA is sensitive to the quality of structural data in interface areas. Relatively modest (0.5-1Å) displacements may have a considetable effect on the binding energy calculations, by this leading PISA to wrong conclusions.
   2. oligomeric state may be measured in chemical conditions that are sufficiently different from those in crystallisation buffer to induce changes in the state.
   3. crystallisation was essentially stimulated by using strong precipitation agents, such as metal ions, which effectively produce additional binding. As a result, PISA can suggest a higher oligomeric state. In order to check this hypothesis, exclude precipitation agents from PISA analyses, as explained here.
   4. crystallised protein is a mutant. Sometimes, even moderate mutations may lead to changing oligomeric state, even if those mutations are not found in interface areas. Removal part of protein sequence may change the oligomeric state, too.
   5. part of structure is disordered and is not seen in electron density. For PISA, this is equivalent to the modification (mutation) of the protein, which may result in changing oligomeric state.
   6. oligomeric state corresponds to weakly bound complex. Such complex may get re-assembled in the course of crystallisation, with probability depending exponentially on the free Gibbs energy of dissociation (cf the corresponding publication (E. Krissinel (2010)).
   7. the particular oligomeric state is expected to be there only in certain concentration range. PISA's summary pages present assemblies in "average conditions", which include unspecified concentration. However, by inspecting the concentration profile of assembly stock, the correct answer may be found sometimes.