Topics

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Expression and Purification

• Expression systems
• Tags
• Expression screening
• Purification
• Cleavage: wanted and unwanted
• DNA and DNA-binding proteins
• Expression and Purification: Tips and Tricks

Crystals

Crystal growth and manipulation

• Modifying the protein to crystallize better
• Crystallization screens and methods
• Robots for crystallization setup
• Visualization of crystal growth
• Robots for crystal mounting
• Crystal growth: Tips and Tricks

Data collection

• Synchrotron beamlines
• Cryo
• Strategies
• Data quality
• Radiation damage
• Data collection: Tips and Tricks

Crystallography

Theory

• Basics of Crystallography
• Phase problem, and Phasing
• R-factors
• References and links

Programs

by package

(large packages first)

• CCP4
• CNS
• PHENIX
• SHELX C/D/E/L (homepage at [1])
• moleman, lsqman, ... from Uppsala Software Factory
• XDS homepage and XDSwiki
• HKL homepage
• COOT
• PyMol wiki
• O
• ARP/wARP
• SHARP homepage
• ...

by task

• Data reduction
• Molecular replacement (MR)
• Experimental phasing (SIR/MIR and SAD/MAD)
• Model building
• Refinement
• Model validation
• Solving a structure: Tips and Tricks
• Model building and refinement: Tricks and Tips

Bioinformatics

• Servers and programs for sequence analysis (e.g. alignment)
• Servers and programs for protein structure analysis
• Servers for ligand topologies/parameters
• Prediction of structure from sequence: servers and programs
• Programs for visualization (see also Model building)
• Links to Bioinformatics websites

Hardware: computing and displaying

• Computer hardware
• Operating systems and Linux distributions
• Graphics cards and 3D

FAQ and troubleshooting

• protein is not expressed or cannot be purified
• crystals don't grow
• phases too bad
• model does not refine