Crystallization & Production of Proteins
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Useful Reference Papers
Tips on crystallizing a Protein-DNA complex
1. Schultz, S. C., Shields, G. C. & Steitz, T. A. (1990).
Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. J. Mol.
Biol. 213, 159–166.
2. Tan et al, Crystallization of the Yeast MATa2/MCM1/DNA Ternary Complex: General Methods and
Principles for Protein/DNA Cocrystallization J. Mol. Biol. (2000) 297, 947±959
3. Cannone et al, Crystallization of bFGF-DNA aptamer complexes using a
Sparse Matrix designed for protein–nucleic acid complexes Journal of Crystal Growth, 2001 232
(2001) 409–417
SAD Phasing
1. Lott JS et al. (2003) Acta Cryst D Biol Crystallogr, Dec (Pt 12): 2242-6. Making the most of two
crystals: structural analysis of a conserved hypothetical protein using native gel screening and SAD
phasing.
Crystallization Suppliers
Hampton Research Emerald Biosystems
Qiagen Molecular Dimensions Ltd.
Jena Bioscience Microlytic
Amino acid analysis for determination of SeMet incorporation in a
recombinant protein
Proton Induced X-ray Emission: Contact Dr. Chris Jeynes for this service
Yale University: amino acid analysis for Se-Met incorporation in protein samples
MALDI-TOF determination of Se-Met incorporation: Grenoble Paris
Models of Structures
BIO-ETCH - 3D protein structure data laser-etched into optical crystal.
Construct Design Servers
Design efficiently truncation constructs to facilitate protein expression and crystallization trials - The
Netherlands Cancer Institute
CODON Optimization Servers
OPTIMIZER: on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression
level.
Rare Codon Caltor: (Programmed by Edmund Ng)
Useful Tools and Information
BMCD - The Biological Macromolecule Crystallization Database contains crystal data and the
crystallization conditions, which have been compiled from literature.
The capillary top free crystal mounting method - Nobuhisa Watanabe
Cryoprotection of delicate crystals - Artem Evdokimov's humble recipe.
Cryo-protectant Strategy - Roger S. Rowlett's protocol
Crystal Screen Tables - To help keep track of initial crystallization trials.
Crystal Screen Wizard - GUI to calculate 2D gradients for crystal screen optimization (P. Hubbard)
Crystallization protocols (Johan Zeelen)
DISOPRED - Server to predict areas of disorder that may be hampering crystallization. To submit a
job - click here.
FROCIVANTO - Server to help create fragment cocktails.
GE Healthcare Life Science Handbooks: Helpful advice particularly in Protein Purification,
Handbook and in Ion Exchange Chromatography: Principles and methods.
HATODAS - a WWW-based tool designed to assist the heavy-atom derivatization of proteins.
Heavy Atom Databank - information on HEAVY-ATOM derivatives of protein crystals.
Heavy Atom Reactivity Prediction - Peter Sun's NIAID site
Heavy Atom Derivative Tutorial - Accumulation of information about heavy atom derivatives.
JAXA - Cryoprotectant database for protein crystals.
Making Se-Met proteins in non-auxotrophic E.coli - Artem Evdokimov
Membrane Proteins: references for purification & crystallization
Membrane Protein Data Bank (MPDB) - An on-line, searchable, relational database with select
structural and functional information on membrane proteins and peptides. Searchable on-line by
protein characteristic, structure method, crystallization technique, detergent, temperature, pH, author,
etc.
Microseed matrix-screening method for protein crystallization
NAID's Ranking of most reactive derivative compounds
Optimizing Expression Levels - EMBL Hamburg site.
PFG - A recipe calculator for thermodynamically correct buffers for pH control.
Pictorial library of crystallization drop phenomena (Terese Bergfors, Uppsala University)
Protein Crystallization (Structural Medicine Protein Crystallography Course)
Removing Crystals from Automated Sitting Drop Trays - Artem Evdokimov's advice.
SDsearch - used to find chemical compounds for binding analysis from large vendor collections with
user-defined chemical properties and/or containing specified substructures.
SERp - Suggests mutation candidates that are likely to enhance a protein's crystallizability.
Specific labeling of proteins (e.g. Sel-Met) (Mahavir Singh, UCLA)
Summary of Screens - Screening module of the Cambridge crystallography course.
The Crystal Screen Wizard - X-ray crystallography tools to help you collate and analyze your protein
and DNA crystal screening trials.
Tips and Tricks - Crystallization tips maintained by Dr. Xinhua Ji at NCI.
XtalPred - Prediction of Protein Crystallizability.
Tips on crystallizing a Protein-DNA complex
1. Schultz, S. C., Shields, G. C. & Steitz, T. A. (1990).
Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. J. Mol.
Biol. 213, 159–166.
2. Tan et al, Crystallization of the Yeast MATa2/MCM1/DNA Ternary Complex: General Methods and
Principles for Protein/DNA Cocrystallization J. Mol. Biol. (2000) 297, 947±959
3. Cannone et al, Crystallization of bFGF-DNA aptamer complexes using a
Sparse Matrix designed for protein–nucleic acid complexes Journal of Crystal Growth, 2001 232
(2001) 409–417
SAD Phasing
1. Lott JS et al. (2003) Acta Cryst D Biol Crystallogr, Dec (Pt 12): 2242-6. Making the most of two
crystals: structural analysis of a conserved hypothetical protein using native gel screening and SAD
phasing.
Crystallization Suppliers
Hampton Research Emerald Biosystems
Qiagen Molecular Dimensions Ltd.
Jena Bioscience Microlytic
Amino acid analysis for determination of SeMet incorporation in a
recombinant protein
Proton Induced X-ray Emission: Contact Dr. Chris Jeynes for this service
Yale University: amino acid analysis for Se-Met incorporation in protein samples
MALDI-TOF determination of Se-Met incorporation: Grenoble Paris
Models of Structures
BIO-ETCH - 3D protein structure data laser-etched into optical crystal.
Construct Design Servers
Design efficiently truncation constructs to facilitate protein expression and crystallization trials - The
Netherlands Cancer Institute
CODON Optimization Servers
OPTIMIZER: on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression
level.
Rare Codon Caltor: (Programmed by Edmund Ng)
Useful Tools and Information
BMCD - The Biological Macromolecule Crystallization Database contains crystal data and the
crystallization conditions, which have been compiled from literature.
The capillary top free crystal mounting method - Nobuhisa Watanabe
Cryoprotection of delicate crystals - Artem Evdokimov's humble recipe.
Cryo-protectant Strategy - Roger S. Rowlett's protocol
Crystal Screen Tables - To help keep track of initial crystallization trials.
Crystal Screen Wizard - GUI to calculate 2D gradients for crystal screen optimization (P. Hubbard)
Crystallization protocols (Johan Zeelen)
DISOPRED - Server to predict areas of disorder that may be hampering crystallization. To submit a
job - click here.
FROCIVANTO - Server to help create fragment cocktails.
GE Healthcare Life Science Handbooks: Helpful advice particularly in Protein Purification,
Handbook and in Ion Exchange Chromatography: Principles and methods.
HATODAS - a WWW-based tool designed to assist the heavy-atom derivatization of proteins.
Heavy Atom Databank - information on HEAVY-ATOM derivatives of protein crystals.
Heavy Atom Reactivity Prediction - Peter Sun's NIAID site
Heavy Atom Derivative Tutorial - Accumulation of information about heavy atom derivatives.
JAXA - Cryoprotectant database for protein crystals.
Making Se-Met proteins in non-auxotrophic E.coli - Artem Evdokimov
Membrane Proteins: references for purification & crystallization
Membrane Protein Data Bank (MPDB) - An on-line, searchable, relational database with select
structural and functional information on membrane proteins and peptides. Searchable on-line by
protein characteristic, structure method, crystallization technique, detergent, temperature, pH, author,
etc.
Microseed matrix-screening method for protein crystallization
NAID's Ranking of most reactive derivative compounds
Optimizing Expression Levels - EMBL Hamburg site.
PFG - A recipe calculator for thermodynamically correct buffers for pH control.
Pictorial library of crystallization drop phenomena (Terese Bergfors, Uppsala University)
Protein Crystallization (Structural Medicine Protein Crystallography Course)
Removing Crystals from Automated Sitting Drop Trays - Artem Evdokimov's advice.
SDsearch - used to find chemical compounds for binding analysis from large vendor collections with
user-defined chemical properties and/or containing specified substructures.
SERp - Suggests mutation candidates that are likely to enhance a protein's crystallizability.
Specific labeling of proteins (e.g. Sel-Met) (Mahavir Singh, UCLA)
Summary of Screens - Screening module of the Cambridge crystallography course.
The Crystal Screen Wizard - X-ray crystallography tools to help you collate and analyze your protein
and DNA crystal screening trials.
Tips and Tricks - Crystallization tips maintained by Dr. Xinhua Ji at NCI.
XtalPred - Prediction of Protein Crystallizability.