Wybór_struktury_w_PDB

Introduction - notes

• In the X-ray crystallography of macromolecules, it is difficult to distinguish the difference between H2O and Mg2+ and Na+ (all have 10 electrons)

• the ions are relatively mobile around the uniform backbone of negatively charged phosphates. Hence macromolecular models typically contain a deficit of ions compared to the true ionic strength of the buffer

What are the criteria to choose the best protein structure from PDB

Following are few points to keep in mind while selecting a protein structure from PDB

1. Resolution is a measure of the quality of the data that has been collected on the crystal containing the protein or nucleic acid [...] High-resolution structures, with resolution values of 1 Å or so, are highly ordered and it is easy to see every atom in the electron density map. from PDB101

2. R-value and R-free: measure of the quality of the atomic model obtained from the crystallographic data. When solving the structure of a protein, the researcher first builds an atomic model and then calculates a simulated diffraction pattern based on that model. The R-value measures how well the simulated diffraction pattern matches the experimentally-observed diffraction pattern. A totally random set of atoms will give an R-value of about 0.63, whereas a perfect fit would have a value of 0. Typical values are about 0.20. ... or an ideal model that is not over-interpreting the data, the R-free will be similar to the R-value. Typically, it is a little higher, with a value of about 0.26. from PDB101

3. EDS - jest dostępne? (Electron Density Server at Uppsala University)

4. Domain completeness. Examine your PDB structure and confirm the under study domain full structure availability. Partial domain will lead to false interpretations.

5. Variant /Mutations. According to your case study look for whether your structure is a wild type or a mutant/variant. In case of a mutant structure requirement you may have to introduce required mutations manually and model them.

6. Side Chain Completeness ( is of secondary importance). Structures determined through old techniques might have (Not always) missing side chains due to flaw in tech or manual error. Right 3D confirmation of Side chains is critical in small ligand binding thus ensure their completeness. As a possible solution you may look for latest structure availability of the same.

7. Ligand /Crystalline Water / Co factor presence. To get out the right docking result removal (As per case study ) of these elements form PDB file is important.

8. Search and superimpose high resolution structures of your target and select a structure that is a good representative, i.e, not distorted too far away from the others by, say, a large ligand.