Is the structure of a crystalized protein the native one?
I'll use quotes from B. Rupp, Biomolecular Crystallography (p. 7-8) to answer.

Generally the structure is similar...


  Comparison of many nuclear magnetic resonance (NMR) solution structure
  ensembles with crystallographic structure has shown that the core
  structure of protein molecules remains unchanged compared with the
  solution state during crystallization. In addition, enzymes packed in
  crystals even maintain biological activity.


with some parts not visible in the experiment...


  The maintenance of the core structure and of enzymatic function shows
  that crystal structures are a very good approximation of the native
  protein solution structure. Nonetheless, highly flexible or mobile
  regions, frequently the amino- or carboxyl-termini of the protein chain or 
  flexible loops connecting secondary structure elements, can be
  poorly defined or even absent in the electron density and thus can be
  modeled only with limited confidence.


but beware...


  In certain situation flexible and dynamic regions of a protein
  molecule can be rigidly fixed in a specific conformation as a result
  of crystal packing interactions. In most cases this represents just a
  snapshot of one possible conformation out of many and it must be
  understood that such a specific conformation may not locally represent
  the protein structure in solution. A simple safeguard against
  misinterpretations -- which is usually assignment of certain
  biological relevance to regions where that is de facto not warranted --
  is to display all neighboring, symmetry-related molecules in the crystal
  structure and examine if any intermolecular interactions are
  present that are a result of crystal packing. Such packing induced
  artifacts can also hamper for example drug discovery by altering or
  blocking binding sites and thus preventing an otherwise active
  substance from binding.