Wikiomics:NMR vs. X-ray for structure determination

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For now, this page is just a collection of references which are somehow related to the differences of structures obtained by Wikiomics:NMR or Wikiomics:X-ray crystallography, but of course any additional information on the topic is welcome.


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  18. Skrynnikov NR, Goto NK, Yang D, Choy WY, Tolman JR, Mueller GA, and Kay LE. Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin. J Mol Biol. 2000 Feb 4;295(5):1265-73. DOI:10.1006/jmbi.1999.3430 | PubMed ID:10653702 | HubMed [SGY+00]
  19. Doreleijers JF, Rullmann JA, and Kaptein R. Quality assessment of NMR structures: a statistical survey. J Mol Biol. 1998 Aug 7;281(1):149-64. DOI:10.1006/jmbi.1998.1808 | PubMed ID:9680482 | HubMed [DRK98]
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  21. Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, and Bonvin AM. RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins. 2005 Jun 1;59(4):662-72. DOI:10.1002/prot.20408 | PubMed ID:15822098 | HubMed [NDV+05]
  22. Fan H and Mark AE. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins. 2003 Oct 1;53(1):111-20. DOI:10.1002/prot.10496 | PubMed ID:12945054 | HubMed [FM03]
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  24. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, and Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D226-9. DOI:10.1093/nar/gkh039 | PubMed ID:14681400 | HubMed [AHB+04]
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  26. Rai N, Nöllmann M, Spotorno B, Tassara G, Byron O, and Rocco M. SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics. Structure. 2005 May;13(5):723-34. DOI:10.1016/j.str.2005.02.012 | PubMed ID:15893663 | HubMed [RNS+05]
  27. Hooft RW, Sander C, Scharf M, and Vriend G. The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput Appl Biosci. 1996 Dec;12(6):525-9. PubMed ID:9021272 | HubMed [HSS+96]
  28. Doreleijers JF, Vriend G, Raves ML, and Kaptein R. Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature. Proteins. 1999 Nov 15;37(3):404-16. PubMed ID:10591100 | HubMed [DVR+99]
  29. Spronk CAEM, Nabuurs SB, Krieger E, Vriend G, and Vuister GW. Validation of protein structures derived by NMR spectroscopy. Progress in Nuclear Magnetic Resonance Spectroscopy 2004; 45(3-4) 315-337. [spronk2004]
  30. Nabuurs SB, Spronk CA, Vuister GW, and Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol. 2006 Feb;2(2):e9. DOI:10.1371/journal.pcbi.0020009 | PubMed ID:16462939 | HubMed [nabuurs2006]
  31. Philippopoulos M and Lim C. Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI. Proteins. 1999 Jul 1;36(1):87-110. PubMed ID:10373009 | HubMed [Philippopoulos]
All Medline abstracts: PubMed | HubMed