Difference between revisions of "Crystallography"

From CCP4 wiki
Jump to navigationJump to search
Line 46: Line 46:
 
* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]
 
* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]
 
* [http://tuna.tamu.edu/ Bias removal server]
 
* [http://tuna.tamu.edu/ Bias removal server]
* [http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp York suite (Balbes, Modsearch, Zanuda)]
+
* York suite (Balbes, Modsearch, [https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Zanuda])
 
* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]
 
* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]
 
* [http://iterate.sourceforge.net/  Bravais Lattice Determination by Projections]
 
* [http://iterate.sourceforge.net/  Bravais Lattice Determination by Projections]

Revision as of 18:35, 20 March 2020

Crystallographic Theory

Procedures

Crystallography Software

For Specific Tasks

Automated Pipelines for Structure Solution

Web services

Software Packages

(large packages first)

Libraries for crystallography and related areas

Tips and Tricks

Teaching crystallography

Crystallography courses on the web

Crystallography books

Test data sets

The effect of resolution on electron density

  • James Holton's movie [[4]]

Understanding and extending the properties and limitations of crystallographic computations

Ensemble refinement, and molecular dynamics

  1. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [5]
  2. Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [6]
  3. Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [7]
  4. 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) [8] (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

  1. 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) [9]

NMR versus X-ray

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

  1. Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [10]
  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. [11]