1. 1 Protein Crystallization Database: Database Design Douglas S. Kerr & Vadim Cherezov July 15, 2002

2. Protein Crystallization Database2 Protein Crystallization Screening multidimensional space Variables: - Temperature - Precipitants (~100) In practice, combinations of no more than 5 variables + limits on concentrations

3. July 15, 2002Protein Crystallization Database3 Crystallization Database Structure Inventories Records of crystallization setups Records of observations

4. July 15, 2002Protein Crystallization Database4 Crystallization Database features Keeps track of everything Flexible (not limited to only one method) Scoring scheme for analysis Power to predict

5. July 15, 2002Protein Crystallization Database5 The basic idea A plate with multiple cells is used. One “protein mixture” is created for the plate containing Protein(s) Lipid(s) Buffer(s) Detergent(s) Precipitant(s)

6. July 15, 2002Protein Crystallization Database6 The basic idea, continued A different screen is used in each cell. Observations are made over time. At each time, each cell is given a “score” referring to the quality of any possible crystals formed.

7. July 15, 2002Protein Crystallization Database7 Stocks of the Various Materials Stocks may be Purchased or Created in the Lab. Source of Purchased Stock is recorded. Experimentor of Created Stock is recorded. The composition of each stock is recorded.

8. July 15, 2002Protein Crystallization Database8 Stock Types Proteins Lipids (Natural & Synthetic) Buffers Detergents Precipitants Chemicals (Used to create) Buffers Precipitants Protein Mixtures Screens

9. July 15, 2002Protein Crystallization Database9 The Database Design: 8 Subschemata 7 Stocks Chemicals and Precipitants Detergents Buffers Lipids Proteins Screens Protein Mixtures Observations

10. July 15, 2002Protein Crystallization Database10 Chemical and Precipitant Stocks Chemical Stocks are Purchased Precipitant Stocks Created from 1 or more Chemical Stocks. Purchased. The Source of any Purchased Stocked is recorded. The Experimentor creating any Created Stocked is recorded.

11. July 15, 2002Protein Crystallization Database11 Chemical and Precipitant Stocks Dry (T/F) H 2 0/D 2 O % Both Created and Purchased Chemical Names Chemical Stocks For postscript and PDF versions of this and the other subschemata, see http://www.cis.ohio-state.edu/~doug/Lipidat/Crystallization/. http://www.cis.ohio-state.edu/~doug/Lipidat/Crystallization/

12. July 15, 2002Protein Crystallization Database12 One-to-Many Relationship: Chemicals to Chemical_Stocks

13. July 15, 2002Protein Crystallization Database13 Buffer Stocks 1 Main Reagent 0 (?) or 1 Titrant 0 or more Detergents 0 or more Chemical Additives

14. July 15, 2002Protein Crystallization Database14 Buffer Stocks Many-to-Many Relationship: The same Detergent Stock may be used in several Buffers. A buffer Stock may contain several detergents. Both the Main Reagent and Titrant are Chemicals.

15. July 15, 2002Protein Crystallization Database15 Many-to-Many Relationship: Chemicals to Buffer_Stocks_purchased 1 1 1   

16. July 15, 2002Protein Crystallization Database16 Detergent Stocks Purchased Created 1 or more Purchased Detergent Stocks

17. July 15, 2002Protein Crystallization Database17 Detergent Stocks May combine several Purchased Detergents to create a Detergent Stock

18. July 15, 2002Protein Crystallization Database18 Lipid Stocks 1 Synthetic Lipid Or 1 Natural Lipid

19. July 15, 2002Protein Crystallization Database19 Lipid Stocks Synthetic Lipid Natural Lipid

20. July 15, 2002Protein Crystallization Database20 Protein Stocks 1 Protein Identified by its Source Organism Organism Type and Extract Type 0 or more Detergents 1 or more Lipids 0 or more Additives 0 or 1 Buffer

21. July 15, 2002Protein Crystallization Database21 Protein Stocks The Protein Purchased Created

22. July 15, 2002Protein Crystallization Database22 Protein Mixtures Composition 1 Protein Stock May already contain Lipid(s) 1 or more Lipids 1 or more Detergents 1 Buffer, in addition to one in the Protein Stock Crystallization Method(s)

23. July 15, 2002Protein Crystallization Database23 Protein Mixtures

24. July 15, 2002Protein Crystallization Database24 Screen Stocks 1 or more Detergents 1 Buffer 1 or more Precipitants

25. July 15, 2002Protein Crystallization Database25 Screen Stocks Purchased Created

26. July 15, 2002Protein Crystallization Database26 Observations Collected by Plate. 1 Protein Mixture 1 Scoring Scheme Different Schemes may be used with different plates. Several Wells on a Plate. Different Screen and/or Screen Concentration for each Well. Observations repeated over time, giving a Score each time. Different Scoring Schemes may exist.

27. July 15, 2002Protein Crystallization Database27 Observations Each Plate has many Wells. Each Well has many Observations. 1 Experimentor sets up the Plate. Different Experimentors may observe the plate.