P212121

The PDB can be pretty intimidating when it comes to extracting information. I still have issues with its search capabilities, which may lead you to think that generating structural statistics is very hard. Thats where the site PDBeStatistics can be of great help.

How does your structure compare with those already deposited into the PDB?

For example, how does the difference between your Rfactor and Rfree (Rdiff) compare against other structures at the same resolution?

To generate this graph:
1) Under Experiment: Resolution
2) Second parameter: Xtal: Rdiff
3) Click on desired area: In this case it is a resolution of 2.5 (currently 807 structures, highlighted in magenta). The Rdiff is displayed along the right hand side, in this case 0.035

You can adjust the range displayed using the slider in ‘Truncate Graph’ (center of graph in blue)


Here is another example displaying the percent solvent distribution across the PDB:


This site can also serve as an excellent resource for presentations. Hey, had to do it

Thanks to Tom for developing this site and bringing it to our attention.

Related Posts:

• A Roundtable Discussion on the Work of Max Perutz
• PCDB: Protein Conformational Database
• LIGPLOT: Plotting Protein-Ligand Interactions
• A Web Interface for PDB Databases
• Big Crystals

2 Awesome Insights so far | Have Your Say!

1. 

   Oliver Clarke
   October 22nd, 2009 at 9:07 PM #

   This is great! Thanks for posting it, I’d been looking for an easy way to extract stats from the PDB for a while.

2. 

   Sean
   October 27th, 2009 at 9:46 AM #

   Hello Oliver,

   One of my goals is to bring to light helpful tools that others may not even know exist. I am able to track statistics about which posts seem to be popular and/or helpful, but leaving a comment or email means a lot more. It means that you took time out of your day to give me feedback and I really appreciate it.