The PDB is an archive of experimentally determined structures of biological macromolecules and their complexes with each other or with small molecule ligands (e.g., ions, cofactors, inhibitors, and drugs). All structures in the archive began with a physical sample of the molecules being studied experimentally. Data collected from the experiment(s) were then used to compute a 3D model of the molecule(s). Note: the archive also includes a small number of computationally modeled structures that were submitted to PDB prior to October 2006. Read more about this community decision.

The Experiment tab presents details about the experimental procedures and constraints used in solving the structure you are exploring.

What is the Experiment?

The majority of structures in the PDB were determined using X-ray crystallography, Nuclear Magnetic Resonance (NMR), or Electron Microscopy (3DEM). Structures determined using other methods such as neutron diffraction, electron crystallography, solution scattering, and those determined using multiple methods are also archived in the PDB. Learn more about the types of experimentally determined structures in the PDB.

Why learn about the Experiment?

Learning about the experiment tells you the conditions, constraints, and assumptions made during sample preparation, data collection, and data analysis. Knowing this can inform you about the reliability of the results reported.


The Interface

Although a quick overview of the experimental methods is presented on the Structure Summary page, more detailed information is provided here. Depending on the experimental method used, specific types of information are presented on the Experiments page. Examples for the three most common types experiments are listed below:

  • For X-ray structures
    • Crystal (unit cell dimensions) and crystallization details
    • Data collection site and details
    • Refinement methods, software used, and structure quality
    • See an example here.
  • For NMR structures
    • Types of NMR experiments done and solution conditions used
    • Spectrometer(s) used for data collection
    • Refinement methods, software used and model details
    • See an example here.
  • For 3DEM structures
    • Sample preparation details
    • Data collection instrument(s), methods, and details
    • Data analysis, 3D reconstructions software and details
    • Model-fitting and refinement details
    • See an example here.

Learning about the Structure

The experimental details provide a context for how the sample or samples were prepared, how data were collected, and how the data were analyzed for the purpose of computing the model coordinates. Understanding this information can help you decide how useful the structural data will be for answering your specific questions. It can also provide details to help you either duplicate the experiment and/or plan the structure determination of a related sample.

A few examples of what more you can learn about a structure include:

  • In the case of an X-ray structure, information about the starting model (if the structure was solved by molecular replacement), resolution limits, R-factor, etc. can help you examine model quality, model bias, and other details.
  • In the case of an NMR structure, knowing which experiments were performed to gather data can provide insights about which experiments may be relevant for you to learn more about the samples you are preparing and molecules and systems you are studying.

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Last updated: 11/19/2021