Difference between revisions of "Crystallography"

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* [http://www.solve.lanl.gov/index.html Solve/Resolve]
 
* [http://www.solve.lanl.gov/index.html Solve/Resolve]
 
* [http://rna.ucsc.edu/pdbrestraints/ PDB coordinates to Restraints] - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.
 
* [http://rna.ucsc.edu/pdbrestraints/ PDB coordinates to Restraints] - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.
 +
* [https://www.globalphasing.com/ Global Phasing Ltd] (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO)
  
 
=== Libraries for crystallography and related areas ===
 
=== Libraries for crystallography and related areas ===

Latest revision as of 13:57, 23 April 2021

Crystallographic Theory[edit | edit source]

Procedures[edit | edit source]

Crystallography Software[edit | edit source]

For Specific Tasks[edit | edit source]

Automated Pipelines for Structure Solution[edit | edit source]

Web services[edit | edit source]

Software Packages[edit | edit source]

(large packages first)

Libraries for crystallography and related areas[edit | edit source]

Tips and Tricks[edit | edit source]

Teaching crystallography[edit | edit source]

Crystallography courses on the web[edit | edit source]

Crystallography books[edit | edit source]

Test data sets[edit | edit source]

The effect of resolution on electron density[edit | edit source]

  • James Holton's movie [[4]]

Understanding and extending the properties and limitations of crystallographic computations[edit | edit source]

Ensemble refinement, and molecular dynamics[edit | edit source]

  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[edit | edit source]

  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[edit | edit source]

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]