1 protein crystallization database: database design douglas s. kerr & vadim cherezov july 15,...

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Protein Crystallization Database: Database Design

Douglas S. Kerr & Vadim Cherezov

July 15, 2002

July 15, 2002 Protein Crystallization

Database 2

Protein Crystallization

Screening multidimensional space

Variables:- Temperature- Precipitants (~100)

In practice, combinations of no more than 5 variables

+ limits on concentrations


Database 3

Crystallization Database Structure

Inventories Records of crystallization setups Records of observations


Database 4

Crystallization Database features

Keeps track of everything Flexible (not limited to only one

method) Scoring scheme for analysis Power to predict


Database 5

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)


Database 6

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.


Database 7

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.


Database 8

Stock Types Proteins Lipids (Natural &

Synthetic) Buffers Detergents Precipitants

Chemicals (Used to create) Buffers Precipitants

Protein Mixtures Screens


Database 9

The Database Design:8 Subschemata 7 Stocks

Chemicals and Precipitants Detergents Buffers Lipids Proteins Screens

Protein Mixtures Observations


Database 10

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.


Database 11

Chemical and Precipitant Stocks

Dry (T/F)

H20/D2O %

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/.


Database 12

One-to-Many Relationship:Chemicals to Chemical_Stocks

Chemical_StocksChemical_Stock_ID Chemical_ID Batch_Number Date Source_ID Dry H2O_Percentage Concentration Concentration_Units pH Footnotes

1 1 S243_34_L 3/12/02 Sigma Y2 1 F153_121 5/20/02 Fisher N 100 4 M3 1 F163_31 6/10/02 Fisher Y

Chemicals_LChemical_ID Chemical_Name

1 Sodium chloride2 Magnesium chloride3 Sodium acetate4 Ammonium phosphate5 Sodium di-hydrogen phosphate6 Sodium hydroxide7 Acetic acid8 Na Tris9 HCl


Database 13

Buffer Stocks 1 Main Reagent 0 (?) or 1 Titrant 0 or more Detergents 0 or more Chemical Additives


Database 14

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.


Database 15

Chemicals_LChemical_ID Chemical_Name

1 Sodium chloride2 Magnesium chloride3 Sodium acetate4 Ammonium phosphate5 Sodium di-hydrogen phosphate6 Sodium hydroxide7 Acetic acid8 Na Tris9 HCl

Additive_in_Buffer_Stock_PurchasedAdditive_ID Buffer_Stock_ID Concentration Concentration_Units

2 1 20 mM4 1 50 mM2 2 20 mM2 3 30 mM1 3 50 mM4 3 20 mM

Buffer_Stock_PurchasedBuffer_Stock_ID Buffer_ID Batch_Number Date Source_ID Main_Reagent_ID Titrant_ID H2O_Percentage Main_Reagent_Concentration Concentration_Units pH Footnotes

1 Phosphate Ph345_2 3/23/02 4 5 6 100 0.1 M 6.52 Acetate Ac433_K 4/28/02 4 3 7 100 0.5 M 4.63 Tris T343_11_2 5/11/02 5 8 9 100 0.5 M 7.4

Many-to-Many Relationship:Chemicals to Buffer_Stocks_purchased

1

1

1


Database 16

Detergent Stocks Purchased Created

1 or more Purchased Detergent Stocks


Database 17

Detergent Stocks

May combine several Purchased Detergents to create a Detergent Stock


Database 18

Lipid Stocks 1 Synthetic Lipid Or 1 Natural Lipid


Database 19

Lipid Stocks

Synthetic Lipid

Natural Lipid


Database 20

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


Database 21

Protein Stocks

The Protein

Purchased

Created


Database 22

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)


Database 23

Protein Mixtures


Database 24

Screen Stocks 1 or more Detergents 1 Buffer 1 or more Precipitants


Database 25

Screen Stocks

Purchased

Created


Database 26

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.


Database 27

ObservationsEach Plate has many Wells.Each Well has many Observations.

1 Experimentor sets up the Plate.Different Experimentors may observe the plate.

1 protein crystallization database: database design douglas s. kerr & vadim cherezov july 15,...

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