Electron density sharpening as a general technique in crystallographic studies

Journal of Molecular Biology

Volumn 426, Issue 4, 2014, Pages 980-993

  Liu, Chang ^a   Xiong, Yong ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

anisotropic correction; automated model building; B factor sharpening; model bias tolerance; phase error tolerance

Indexed keywords

AMINO ACID; CORTICOTROPIN RELEASING FACTOR; LIGAND; MALTOSE BINDING PROTEIN;

ANISOTROPY; ARTICLE; CRYSTAL STRUCTURE; DIFFRACTION; ELECTRON; ELECTRON DENSITY SHARPENING; MACROMOLECULE; PRIORITY JOURNAL; STRUCTURE ANALYSIS; TEMPERATURE; X RAY CRYSTALLOGRAPHY; ANALYTIC METHOD; CONTROLLED STUDY; CRYSTAL; CRYSTALLOGRAPHY; DENSITY; PROTEIN DATA BANK;

ADP; ANISOTROPIC CORRECTION; ATOMIC DISPLACEMENT PARAMETER; AUTOMATED MODEL BUILDING; B-FACTOR SHARPENING; CORTICOTROPIN-RELEASING FACTOR; CRF; FIGURE OF MERIT; FOM; MALTOSE BINDING PROTEIN; MBP; MODEL-BIAS TOLERANCE; MOLECULAR REPLACEMENT; MR; PHASE ERROR TOLERANCE; SA; SIMULATED ANNEALING;

ANISOTROPY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ELECTRONS; MALTOSE-BINDING PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; RECEPTORS, CORTICOTROPIN-RELEASING HORMONE;

EID: 84893662498     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.11.014     Document Type: Article

References (50)

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig et al. The Protein Data Bank Nucleic Acids Res 28 2000 235 242 (Pubitemid 30047768)
2. A. Wilson Determination of absolute from relative X-ray intensity data Nature 150 1942 151 152
3. D. Cruickshank The analysis of the anisotropic thermal motion of molecules in crystals Acta Crystallogr 9 1956 754 756
4. J.D. Dunitz, E.F. Maverick, and K.N. Trueblood Atomic motions in molecular crystals from diffraction measurements Angew Chem Int Ed Engl 27 1988 880 895
5. K.N. Trueblood, H.B. Burgi, H. Burzlaff, J.D. Dunitz, C.M. Gramaccioli, and H.H. Schulz et al. Atomic displacement parameter nomenclature. Report of a subcommittee on atomic displacement parameter nomenclature Acta Crystallogr Sect A Found Crystallogr 52 1996 770 781 (Pubitemid 126474040)
6. S. Sheriff, and W.A. Hendrickson Description of overall anisotropy in diffraction from macromolecular crystals Acta Crystallogr Sect A Found Crystallogr 43 1987 118 121
7. R.W. Grosse-Kunstleve, and P.D. Adams On the handling of atomic anisotropic displacement parameters J Appl Crystallogr 35 2002 477 480
8. M. Strong, M.R. Sawaya, S. Wang, M. Phillips, D. Cascio, and D. Eisenberg Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis Proc Natl Acad Sci USA 103 2006 8060 8065 (Pubitemid 43801052)
9. A.L. Patterson A direct method for the determination of the components of interatomic distances in crystals Z Kristallogr 90 1935 517 542
10. J. Wunderlich A new expression for sharpening Patterson functions Acta Crystallogr 19 1965 200 202
11. M.G. Rossmann, and E. Arnold Patterson and molecular-replacement techniques Int Tables Crystallogr B 2006 235 263
12. T. Stehle, S.J. Gamblin, Y. Yan, and S.C. Harrison The structure of simian virus 40 refined at 3.1 Å resolution Structure 4 1996 165 182 (Pubitemid 126658980)
13. B. DeLaBarre, and A.T. Brunger Considerations for the refinement of low-resolution crystal structures Acta Crystallogr Sect D Biol Crystallogr 62 2006 923 932 (Pubitemid 44125670)
14. A.T. Brunger, B. DeLaBarre, J.M. Davies, and W.I. Weis X-ray structure determination at low resolution Acta Crystallogr Sect D Biol Crystallogr 65 2009 128 133
15. A.L. Patterson A Fourier series method for the determination of the components of interatomic distances in crystals Phys Rev 46 1934 372 376
16. E.W. Hughes The crystal structure of melamine J Am Chem Soc 63 1941 1737 1752
17. G.N. Murshudov, G.J. Davies, M. Isupov, S. Krzywda, and E.J. Dodson The effect of overall anisotropic scaling in macromolecular refinement CCP4 Newsletter on Protein Crystallography 35 1998 37 42
18. P.V. Afonine, R.W. Grosse-Kunstleve, N. Echols, J.J. Headd, N.W. Moriarty, and M. Mustyakimov et al. Towards automated crystallographic structure refinement with phenix.refine Acta Crystallogr Sect D Biol Crystallogr 68 2012 352 367
19. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve et al. Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr Sect D Biol Crystallogr 54 1998 905 921
20. A.T. Brunger Version 1.2 of the crystallography and NMR system Nat Protoc 2 2007 2728 2733
21. G.N. Murshudov, P. Skubak, A.A. Lebedev, N.S. Pannu, R.A. Steiner, and R.A. Nicholls et al. REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr Sect D Biol Crystallogr 67 2011 355 367
22. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J Appl Crystallogr 40 2007 658 674 (Pubitemid 47080256)
23. A.T. Brünger, J. Kuriyan, and M. Karplus Crystallographic R factor refinement by molecular dynamics Science 235 1987 458 460 (Pubitemid 17009580)
24. A.T. Brunger, and P.D. Adams Molecular dynamics applied to X-ray structure refinement Acc Chem Res 35 2002 404 412
25. R.A. Nicholls, F. Long, and G.N. Murshudov Low-resolution refinement tools in REFMAC5 Acta Crystallogr Sect D Biol Crystallogr 68 2012 404 417
26. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.H. Zwart, and L.-W. Hung et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Acta Crystallogr Sect D Biol Crystallogr 64 2008 61 69 (Pubitemid 350308678)
27. Y. Fang, H. Jayaram, T. Shane, L. Kolmakova-Partensky, F. Wu, and C. Williams et al. Structure of a prokaryotic virtual proton pump at 3.2 Å resolution Nature 460 2009 1040 1043
28. C. Chothia, and A.M. Lesk The relation between the divergence of sequence and structure in proteins EMBO J 5 1986 823 826
29. K. Cowtan "dm": an automated procedure for phase improvement by density modification Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31 1994 34 38
30. N.S. Pannu, and R.J. Read Improved structure refinement through maximum likelihood Acta Crystallogr Sect A Found Crystallogr 52 1996 659 668 (Pubitemid 126474027)
31. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr Sect D Biol Crystallogr 53 1997 240 255 (Pubitemid 27235885)
32. A. McCoy Liking likelihood Acta Crystallogr Sect D Biol Crystallogr 60 2004 2169 2183 (Pubitemid 41742769)
33. J. Karle, and H. Hauptman Application of statistical methods to the naphthalene structure Acta Crystallogr 6 1953 473 476
34. V. Subramanian, and S.R. Hall Normalized structure factors. I. Choice of scaling function Acta Crystallogr Sect A Cryst Phys Diffr Theor Gen Crystallogr 38 1982 577 590
35. K. Cowtan The Buccaneer software for automated model building. 1. Tracing protein chains Acta Crystallogr Sect D Biol Crystallogr 62 2006 1002 1011 (Pubitemid 44337374)
36. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, and N. Echols et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr Sect D Biol Crystallogr 66 2010 213 221
37. H. Yang, J. Wang, X. Jia, M.W. McNatt, T. Zang, and B. Pan et al. Structural insight into the mechanisms of enveloped virus tethering by tetherin Proc Natl Acad Sci 107 2010 18428 18432
38. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr Sect D Biol Crystallogr 50 1994 760 763
39. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of Coot Acta Crystallogr Sect D Biol Crystallogr 66 2010 486 501
40. Y. Xiong, F. Li, J. Wang, A.M. Weiner, and T.A. Steitz Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes Mol Cell 12 2003 1165 1172 (Pubitemid 37492930)
41. Y. Xiong, and T.A. Steitz Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template Nature 430 2004 640 645 (Pubitemid 39061672)
42. B. Pan, Y. Xiong, and T.A. Steitz How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA Science 330 2010 937 940
43. V. Schomaker, and K.N. Trueblood On the rigid-body motion of molecules in crystals Acta Crystallogr Sect B Struct Crystallogr Cryst Chem 24 1968 63 76
44. M.D. Winn, M.N. Isupov, and G.N. Murshudov Use of TLS parameters to model anisotropic displacements in macromolecular refinement Acta Crystallogr Sect D Biol Crystallogr 57 2001 122 133 (Pubitemid 32062682)
45. R.C. Agarwal A new least-squares refinement technique based on the fast Fourier transform algorithm Acta Crystallogr Sect A Cryst Phys Diffr Theor Gen Crystallogr 34 1978 791 809
46. L.F. Ten Eyck Crystallographic fast Fourier transforms Acta Crystallogr Sect A Cryst Phys Diffr Theor Gen Crystallogr 29 1973 183 191
47. G.J. Kleywegt, and T.A. Jones xdlMAPMAN and xdlDATAMAN: programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets Acta Crystallogr Sect D Biol Crystallogr 52 1996 826 828 (Pubitemid 27064307)
48. M.D. Winn, C.C. Ballard, K.D. Cowtan, E.J. Dodson, P. Emsley, and P.R. Evans et al. Overview of the CCP4 suite and current developments Acta Crystallogr Sect D Biol Crystallogr 67 2011 235 242
49. K. Cowtan Fitting molecular fragments into electron density Acta Crystallogr Sect D Biol Crystallogr 64 2008 83 89
50. S. French, and K. Wilson On the treatment of negative intensity observations Acta Crystallogr Sect A Cryst Phys Diffr Theor Gen Crystallogr 34 1978 517 525