Crystallography: Difference between revisions
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== Understanding and extending the properties and limitations of crystallographic computations == | == Understanding and extending the properties and limitations of crystallographic computations == | ||
=== | |||
=== Ensemble refinement, and molecular dynamics === | |||
# Burling et al. 1996 | # Burling et al. 1996 | ||
# | # Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031] | ||
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019] | |||
# 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) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules) | |||
=== | === Electron microscopy and X-ray === | ||
# | # Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8] | ||
=== | === NMR versus X-ray === | ||
A couple of papers analysing and comparing NMR and X-ray methods/structures: | A couple of papers analysing and comparing NMR and X-ray methods/structures: | ||
# Science (1992), vol. 257, p. 961 | # Science (1992), vol. 257, p. 961 | ||
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website. | # X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website. | ||
# 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 | # 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 | ||
Revision as of 18:59, 15 November 2008
Crystallographic Theory
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
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
Understanding and extending the properties and limitations of crystallographic computations
Ensemble refinement, and molecular dynamics
- Burling et al. 1996
- Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [2]
- Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [3]
- 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) [4] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)
Electron microscopy and X-ray
- Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [5]
NMR versus X-ray
A couple of papers analysing and comparing NMR and X-ray methods/structures:
- Science (1992), vol. 257, p. 961
- 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.
- 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