Protein Crystallization Database Database Design Douglas S Kerr

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

Protein Crystallization Screening multidimensional space Variables: - Temperature - Precipitants (~100) In practice, combinations of no more than 5 variables + limits on concentrations July 15, 2002 Protein Crystallization Database 2

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

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

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

The basic idea, continued n n n 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. July 15, 2002 Protein Crystallization Database 6

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

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

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

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

Chemical and Precipitant Stocks For postscript and PDF versions of this and the other subschemata, see http: //www. cis. ohio-state. edu/~doug/Lipidat/Crystallization/. Chemical Stocks Dry (T/F) Both Created and Purchased H 20/D 2 O % Chemical Names July 15, 2002 Protein Crystallization Database 11

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

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

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

Many-to-Many Relationship: Chemicals to Buffer_Stocks_purchased 1 1 1 July 15, 2002 Protein Crystallization Database 15

Detergent Stocks n n Purchased Created n 1 or more Purchased Detergent Stocks July 15, 2002 Protein Crystallization Database 16

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

Lipid Stocks n n 1 Synthetic Lipid Or 1 Natural Lipid July 15, 2002 Protein Crystallization Database 18

Lipid Stocks Synthetic Lipid Natural Lipid July 15, 2002 Protein Crystallization Database 19

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

Protein Stocks Created The Protein Purchased July 15, 2002 Protein Crystallization Database 21

Protein Mixtures n Composition n 1 Protein Stock n n n 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) July 15, 2002 Protein Crystallization Database 22

Protein Mixtures July 15, 2002 Protein Crystallization Database 23

Screen Stocks n n n 1 or more Detergents 1 Buffer 1 or more Precipitants July 15, 2002 Protein Crystallization Database 24

Screen Stocks Created Purchased July 15, 2002 Protein Crystallization Database 25

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

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