Crystallography

Crystallographic Theory

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

Crystallography Software

For Specific Tasks

• Data reduction
• Molecular replacement (MR)
• Substructure determination
• Experimental phasing (SIR/MIR and SAD/MAD)
• Electron density modification
• Automated Model building
• Interactive Model building
• Refinement
• Model validation
• Model Evaluation

Automated Pipelines for Structure Solution

• Ants
• Auto-Rickshaw (Structure determination)
• AutoSHARP
• BALBES
• BNP
• CRANK
• Elves
• MrBUMP
• Phenix
• HKL2MAP

Web services

• ARP/wARP web services (model building)
• Auto-Rickshaw (Structure determination) - see example at xds:1RQW
• Bias removal server
• York suite (Balbes, Modsearch, Zanuda)
• Diffraction Anisotropy Server

Software Packages

(large packages first)

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

Tricks and Tips

• Solving a structure
• Model building and refinement
• Model Evaluation and Interpretation
• Finding symmetry elements in P1

Teaching crystallography

• Crystallography courses on the web
• Test data sets

Understanding and extending the properties and limitations of crystallographic computations

Why is the final R-factor about 20% for macromolecules, but as low as 5% for small molecules?

1. Burling et al. 1996
2. DePriso et al. (2004) Structure 12, 831-838

Molecular dynamics and X-ray

1. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [2]

Crystallography versus NMR

A couple of papers analysing and comparing NMR and X-ray methods/structures:

1. Science (1992), vol. 257, p. 961
2. X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint available from Axel Brunger's "publications" website.
3. Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. http://dx.doi.org/10.1371/journal.pcbi.0020009