Refinement of x-ray crystal structures

Comprehensive Biophysics

Volumn 1, Issue , 2012, Pages 105-115

  Brunger, A T ^a   Adams, P D ^b  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

A priori chemical information; Cross validation; Macromolecular structural studies; Maximum likelihood; Molecular dynamics; Simulated annealing; Torsion angle refinement

Indexed keywords

EID: 84882786109     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-374920-8.00108-9     Document Type: Chapter

References (96)

1. Garman E.F. Radiation damage in macromolecular crystallography: what is it and why should we care?. Acta. Crystallogr. D: Biol. Crystallogr. 2010, 66:339-351.
2. Dauter Z. Efficient use of synchrotron radiation for macromolecular diffraction data collection. Prog. Biophys. Mol. Biol. 2005, 89:153-172.
3. Walden H. Selenium incorporation using recombinant techniques. Acta Crystallogr. D Biol. Crystallogr. 2010, 66:352-357.
4. Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 1991, 254:51-58.
5. Hendrickson W.A. Stereochemically restrained refinement of macromolecular structures. Meth. Enzymol. 1985, 115:252-270.
6. Brunger A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992, 355:472-474.
7. Rice L.M., Brunger A.T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins: Struct. Function Genet. 1994, 19:277-290.
8. Winn M.D., Isupov M.N., Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D: Biol. Crystallogr. 2001, 57:122-123.
9. Pannu N.S., Read R.J. Improved structure refinement through maximum likelihood. Acta Cryst. 1996, A52:659-668.
10. Adams P.D., Pannu N.S., Read R.J., Brunger A.T. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA. 1997, 94:5018-5023.
11. Pannu N.S., Murshudov G.N., Dodson E.J., Read R.J. Incorporation of prior phase information strengthens maximum likelihood structural refinement. Acta Cryst. 1998, D54:1285-1294.
12. Kuriyan J., Ösapay K., Burley S.K., Brunger A.T., Hendrickson W.A., Karplus M. Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins 1991, 10:340-358.
13. Burling F.T., Brunger A.T. Thermal motion and conformational disorder in protein crystal structures: comparison of multi-conformer and time-averaging models. Israel J. Chem. 1994, 34:165-175.
14. Burling F.T., Weis W.I., Flaherty K.M., Brunger A.T. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 1996, 271:72-77.
15. Schröder G.F., Levitt M., Brunger A.T. Super-resolution biomolecular crystallography with low-resolution data. Nature 2010, 464:1218-1222.
16. Silva A.M., Rossmann M.G. The refinement of southern bean mosaic virus in reciprocal space. Acta Cryst. 1985, B41:147-157.
17. Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. 1986, A42:140-149.
18. Bricogne G. A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data. Acta Cryst. 1991, A47:803-829.
19. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. 1997, D53:240-255.
20. Adams P.D., Pannu N.S., Read R.J., Brunger A.T. Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement. Acta Cryst. 1999, D55:181-190.
21. Bricogne G. Bayesian statistical viewpoints on structure determination: basic concepts and examples. Meth. in Enzymol. 1997, 276:361-423.
22. Skubák P., Murshudov G.N., Pannu N.S. Direct incorporation of experimental phase information in model refinement. Acta Crystallogr. D: Biol. Crystallogr. 2004, 60:2196-2201.
23. Rice L.M., Earnest T.N., Brunger A.T. Single wavelength anomalous diffraction phasing revisited. Acta Cryst. 2000, D56:1413-1420.
24. Grosse-Kunstleve R.W., Adams P.D. On the handling of atomic anisotropic displacement parameters. J. Appl. Cryst. 2002, 35:477-480.
25. Brunger A.T. Version 1.2 of the crystallography and NMR system. Nat. Protoc. 2007, 2:2728-2733.
26. Jiang J.S., Brünger A.T. Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 1994, 243:100-115.
27. Phillips S.E. Structure and refinement of oxymyoglobin at 1.6A resolution. J. Mol. Biol. 1980, 142:531-554.
28. DeLaBarre B., Brunger A.T. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat. Struct. Biol. 2003, 10:856-863.
29. DeLaBarre B., Brunger A.T. Nucleotide dependent motion and mechanism of action of p97/VCP. J. Mol. Biol. 2005, 347:437-452.
30. Afonine P.V., Grosse-Kunstleve R.W., Adams P.D. A robust bulk-solvent correction and anisotropic scaling procedure. Acta Cryst. 2005, D61:850-855.
31. Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.-W., Kapral G.J., Grosse-Kunstleve R.W., McCoy A.J., Moriarty N.W., Oeffner R., Read R.J., Richardson D.C., Richardson J.S., Terwilliger T.C., Zwart P.H. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010, D66:213-221.
32. Fenn T.D., Schnieders M.J., Brunger A.T. A smooth and differentiable bulk-solvent model for macromolecular diffraction. Acta Crystallogr. D: Biol. Crystallogr. 2010, 66:1024-1031.
33. Engh R.A., Huber R. Accurate bond and angle parameters for X-ray structure refinement. Acta Cryst. 1991, A47:392-400.
34. Parkinson G., Vojtechovsky J., Clowney L., Brunger A.T., Berman H.M. New parameters for the refinement of nucleic acid containing structures. Acta Cryst. 1996, D52:57-64.
35. Allen F.H., Kennard O., Taylor R. Systematic analysis of structural data as a research technique in organic chemistry. Acc. Chem. Res. 1983, 16:146-153.
36. Tronrud D.E., Berkholz D.S., Karplus P.A. Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Crystallogr. D: Biol. Crystallogr. 2010, 66:834-842.
37. Brunger A.T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science 1987, 235:458-460.
38. Weis W.I., Brünger A.T., Skehel J.J., Wiley D.C. Refinement of the influenza virus hemagglutinin by simulated annealing. J. Mol. Biol. 1990, 212:737-761.
39. Blanc E., Roversi P., Vonrhein C., Flensburg C., Lea S.M., Bricogne G. Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallogr. D: Biol. Crystallogr. 2004, 60:2210-2221.
40. Pearlman D.A., Kim S.-H. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol 1990, 211:171-187.
41. Karplus M., Petsko G.A. Molecular dynamics simulations in biology. Nature 1990, 347:631-639.
42. Brunger A.T., Karplus M., Petsko G.A. Crystallographic refinement by simulated annealing: application to a 1.5Å resolution structure of Crambin. Acta Cryst. 1989, A45:50-61.
43. Brunger A.T., Krukowski A., Erickson J. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Cryst. 1990, A46:585-593.
44. Fujinaga M., Gros P., van Gunsteren W.F. Testing the method of crystallographic refinement using molecular dynamics. J. Appl. Cryst. 1989, 22:1-8.
45. Linge J.P., Williams M.A., Spronk C.A., Bonvin A.M., Nilges M. Refinement of protein structures in explicit solvent. Proteins 2003, 50:496-506.
46. Moulinier L., Case D.A., Simonson T. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum. Acta Crystallogr. D: Biol. Crystallogr. 2003, 59:2094-2103.
47. Fenn T.D., Schnieders M.J., Mustyakimov M., Langan P., Pande V.S., Brunger A.T. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA Hydration. Structure 2011, 19:523-533.
48. Trueblood K.N., Bürgi H.B., Burzlaff H., Dunitz J.D., Gramaccioli C.M., Schulz H.H., Shmueli U., Abrahams S.C. Atomic dispacement parameter nomenclature. Report of a subcommittee on atomic displacement parameter nomenclature. Acta Cryst. 1996, A52:770-781.
49. Dunitz J.D., White D.N.J. Non-rigid-body thermal-motion analysis. Acta Cryst. 1973, A29:93-94.
50. Prince E., Finger L.W. Use of constraints on thermal motion in structure refinement of molecules with librating side groups. Acta Cryst. 1973, B29:179-183.
51. Sheriff S., Hendrickson W.A. Description of overall anisotropy in diffraction from macromolecular crystals. Acta Cryst. 1987, A43:118-121.
52. Hirshfeld F.L. Can X-ray data distinguish bonding effects from vibrational smearing?. Acta Cryst. 1976, A32:239-244.
53. Afonine P. V., Grosse-Kunstleve R. W., Adams P. D. (2005b) The Phenix refinement framework. CCP4 newsletter, July 2005; Contribution 8.
54. Terwilliger T.C., Grosse-Kunstleve R.W., Afonine P.V., Moriarty N.W., Zwart P.H., Hung L.W., Read R.J., Adams P.D. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Cryst. 2008, D64:61-69.
55. Schomaker V., Trueblood K.N. On the rigid-body motion of molecules in crystals. Acta Cryst. 1968, B24:63-76.
56. Painter J., Merritt E.A. A molecular viewer for the analysis of TLS rigid-body motion in macromolecules. Acta Crystallogr. D: Biol. Crystallogr. 2005, 61:465-471.
57. Painter J., Merritt E.A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D: Biol. Crystallogr. 2006, 62:439-450.
58. Diamond R. A real-space refinement procedure for proteins. Acta Cryst. 1971, A27:436-452.
59. Sussman J.L., Holbrook S.R., Church G.M., Kim S.-H. Structure-factor least-squares refinement procedure for macromolecular structure using constrained and restrained parameters. Acta Cryst. 1977, A33:800-804.
60. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. 1976, A32:922-923.
61. Gros P., van Gunsteren W.F., Hol W.G.J. Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. Science 1990, 249:1149-1152.
62. Kuriyan J., Petsko G.A., Levy R.M., Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. J. Mol. Biol. 1986, 190:227-254.
63. Kleywegt G.J., Brunger A.T. Checking your imagination: applications of the free R value. Structure 1996, 4:897-904.
64. Brunger A.T. Free R value: cross-validation in crystallography. Methods Enzym. 1997, 277:366-396.
65. Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 1952, 5:802-881.
66. Brunger A.T., Adams P.D., Rice L.M. Enhanced Macromolecular Refinement by Simulated Annealing. International Tables for Crystallography, Volume F: Macromolecular Crystallography 2001, 375-381. Kluwer Academic Publishers, Dordrecht. M.G. Rossmann, E. Arnold (Eds.).
67. Press W.H., Flannery B.P., Teukolosky S.A., Vetterling W.T. Numerical Recipes 1986, Cambridge University Press, Cambridge, 498-546.
68. Stout G.H., Jensen L.H. X-ray Structure Determination 1989, Wiley, New York.
69. Konnert J.H., Hendrickson W.A. A restrained-parameter thermal-factor refinement procedure. Acta Cryst. 1980, A36:344-350.
70. Jack A., Levitt M. Refinement of large structures by simultaneous minimization of energy and R factor. Acta Crystallogr. 1983, A34:931-935.
71. Tronrud D.E., Ten Eyck L.F., Matthews B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Cryst. 1987, A43:489-501.
72. Tronrud D.E. Conjugate-direction minimization: an improved method for the refinement of macromolecules. Acta Crystallogr. A. 1992, 48:912-916.
73. Agarwal R.C. A new least-squares refinement technique based on the fast Fourier transform algorithm. Acta Cryst. 1978, A34:791-809.
74. Kirkpatrick S., Gelatt C.D., Vecchi M.P. Optimization by simulated annealing. Science 1983, 220:671-680.
75. Laarhoven P.J.M., Aarts E.H.L. Simulated Annealing: Theory and Applications 1987, D. Reidel Publishing Company, Dordrecht.
76. Metropolis N., Rosenbluth M., Rosenbluth A., Teller A., Teller E. Equation of state calculations by fast computing machines. J. Chem. Phys. 1953, 21:1087-1092.
77. Verlet L. Computer 'experiments' on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 1967, 159:98-103.
78. Goldstein H. Classical Mechanics 1980, Addison-Wesley Pub. Co., Reading, Massachusetts. 2nd ed.
79. Abramowitz M., Stegun I. Handbook of Mathematical Functions 1968, Dover Publications, New York, 896.
80. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81:3684-3690.
81. Bae D.-S., Haug E.J. A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems. Mech. Struct. Mach. 1987, 15:359-382.
82. Bae D.-S., Haug E.J. A recursive formulation for constrained mechanical system dynamics: Part II. Closed loop systems. Mech. Struct. Mach. 1988, 15:481-506.
83. Jain A., Vaidehi N., Rodriguez G. A fast recursive algorithm for molecular dynamics simulation. J. Comp. Phys. 1983, 106:258-268.
84. Brunger A.T., Adams P.D., Clore G.M., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., Warren G.L. Crystallography & NMR system (CNS): a new software system for macromolecular structure determination. Acta Cryst. 1998, D54:905-921.
85. Shamoo Y., Krueger U., Rice L.M., Williams K.R., Steitz T.A. Crystal structure of the two RNA-binding domains of human hnRNP A1 at 1.75Å resolution. Nature Struct. Biol. 1997, 3:215-222.
86. Rice L.M., Shamoo Y., Brunger A.T. Phase improvement by multi start simulated annealing refinement and structure factor averaging. J. Appl. Cryst. 1998, 31:798-805.
87. Ling H., Boodhoo A., Hazes B., Cummings M.D., Armstrong G.D., Brunton J.L., Read R.J. Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3. Biochemistry 1998, 37:1777-1788.
88. Bass R.B., Strop P., Barclay M., Rees D.C. Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel. Science 2002, 298:1582-1587.
89. DeLaBarre B., Brunger A.T. Considerations for the refinement of low-resolution crystal structures. Acta Crystallogr. D: Biol. Crystallogr. 2006, 62:923-932.
90. Popov A.N., Bourenkov G.P. Choice of data-collection parameters based on statistic modeling. Acta Crystallogr. 2003, D59:1145-1153.
91. Davies J.M., Brunger A.T., Weis W.I. Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure 2008, 16:715-726.
92. Schröder G.F., Brunger A.T., Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 2007, 15:1630-1641.
93. Diamond R. On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor. Acta Crystallogr. A 1990, 46:425-435.
94. Levitt M., Sander C., Stern P.S. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 1985, 181:423-447.
95. Delarue M., Dumas P. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl. Acad. Sci. USA 2004, 101:6957-6962.
96. Tama F., Miyashita O., Brooks C.L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 2004, 337:985-999.