Difference between revisions of "Crystallography"

 
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* [[Twinning]]
 
* [[Twinning]]
 
* [[R-factors]]
 
* [[R-factors]]
 +
* [[Bulk solvent correction]]
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* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]
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* [[Disorder]]
 
* [[References and links]]
 
* [[References and links]]
 +
 +
== Procedures ==
 +
* [[Solve-TAT|Solving a structure]]
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* [[Solve a small-molecule structure]]
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* [[Buildn-TAT|Model building and refinement]]
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* [[Evaluation-TAT|Model Evaluation and Interpretation]]
  
 
== Crystallography Software ==
 
== Crystallography Software ==
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* [[Model validation]]
 
* [[Model validation]]
 
* [[Model Evaluation]]
 
* [[Model Evaluation]]
 +
* [[Loop modelling]]
  
 
=== Automated Pipelines for Structure Solution ===
 
=== Automated Pipelines for Structure Solution ===
 
*[[Ants]]
 
*[[Ants]]
 
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]
 
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]
*[[AutoSHARP]]
+
*[https://www.globalphasing.com/sharp/ autoSHARP]
 
*[[BALBES]]
 
*[[BALBES]]
 
*[[BNP]]
 
*[[BNP]]
 
*[[CRANK]]
 
*[[CRANK]]
 
*[[Elves]]
 
*[[Elves]]
*[[MrBUMP]]
+
*[[MrBUMP]] - molecular replacement
*[[Phenix]]
+
*[[Phenix]] - comprehensive package
*[[HKL2MAP]]
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*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]
  
 
=== Web services ===
 
=== Web services ===
*[http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]
+
* [http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]
*[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]
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* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107].
 +
* [http://witold.med.virginia.edu/fitmunk/server/ Fitmunk] takes a PDB and MTZ file, and helps to identify your protein by electron density based sequencing, and by fitting different conformations. See https://www.ncbi.nlm.nih.gov/pubmed/26894674 and https://www.ncbi.nlm.nih.gov/pubmed/26660914
 +
* [https://staraniso.globalphasing.org/ STARANISO] analyses, corrects and visualises diffraction data for data anisotropy; see also [https://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi PDBpeep] for deposited PDB entries.
 +
* [http://grade.globalphasing.org/ Grade] to create restraint dictionaries for refinement
  
 
=== Software Packages ===
 
=== Software Packages ===
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* [[COOT]]
 
* [[COOT]]
 
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
 
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
 +
* [[CCP4mg]]
 
* [[O]]
 
* [[O]]
 
* [[ARP/wARP]]
 
* [[ARP/wARP]]
 
* [[SHARP]] [http://www.globalphasing.com homepage]
 
* [[SHARP]] [http://www.globalphasing.com homepage]
 
* [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.
 +
* [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 ===
 +
* [[Clipper]]
 +
* [[cctbx|Crystallographic Toolbox]]
 +
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]
 +
* [[mmdb]]
  
===Tricks and Tips===
+
=== Tips and Tricks ===
* [[Solve-TAT|Solving a structure]]
+
* [[Finding symmetry elements in P1]]
* [[Buildn-TAT|Model building and refinement]]
+
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]
 +
 
 +
== Teaching crystallography ==
 +
=== [[Crystallography courses on the web]] ===
 +
=== [[Crystallography books]] ===
 +
=== [[Test data sets]] ===
 +
=== The effect of resolution on electron density ===
 +
* James Holton's movie [[https://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg]]
 +
 
 +
== Understanding and extending the properties and limitations of crystallographic computations ==
 +
 
 +
=== Ensemble refinement, and molecular dynamics ===
 +
# 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 [http://dx.DOI.org/10.1126/science.271.5245.72]
 +
# 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:
 +
# 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 [http://dx.doi.org/10.1126/science.1502561]
 +
# 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]

Latest revision as of 13:57, 23 April 2021

Crystallographic TheoryEdit

ProceduresEdit

Crystallography SoftwareEdit

For Specific TasksEdit

Automated Pipelines for Structure SolutionEdit

Web servicesEdit

Software PackagesEdit

(large packages first)

Libraries for crystallography and related areasEdit

Tips and TricksEdit

Teaching crystallographyEdit

Crystallography courses on the webEdit

Crystallography booksEdit

Test data setsEdit

The effect of resolution on electron densityEdit

  • James Holton's movie [[4]]

Understanding and extending the properties and limitations of crystallographic computationsEdit

Ensemble refinement, and molecular dynamicsEdit

  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-rayEdit

  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-rayEdit

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]