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Guide to Understanding PDB Data
05/22 
The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education.
Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file? These questions and many others are explored in PDB-101's Guide to Understanding PDB Data. This resource was created to help users navigate through the contents of the archive without having a detailed background in structural biology. Topics cover biological assemblies, molecular graphics programs, R-value and R-free, and more.
Topics include
- Biological Assemblies
- Dealing with Coordinates
- Methods for Determining Structure
- Missing Coordinates and Biological Assemblies
- Molecular Graphics Programs
- Resolution
- R-value and R-free
- Structure Factors and Electron Density
- Primary Sequences and the PDB Format
- Small Molecule Ligands
From Methods for Determining Atomic Structures: Structures of photoactive yellow protein were determined by serial femtosecond crystallography after illumination, capturing the isomerization of the chromophore after it absorbs light. Structures included in this movie include: 5hd3 (ground state), 5hdc (100-400 femtoseconds after illumination), 5hdd (800-1200 femtoseconds), 5hds (3 picoseconds), 4b9o (100 picoseconds), 5hd5 (200 nanoseconds) and 1ts0 (1 millisecond). For more, see Molecule of the Month on Photoactive Yellow Protein.
