메뉴 건너뛰기




Volumn 72, Issue 3, 1999, Pages 245-270

Density modification for macromolecular phase improvement

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT;

EID: 0032872798     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0079-6107(99)00008-5     Document Type: Article
Times cited : (247)

References (53)
  • 1
    • 0030855279 scopus 로고    scopus 로고
    • Bias reduction in phase refinement by modified interference functions: Introducing the gamma correction
    • Abrahams J.P. Bias reduction in phase refinement by modified interference functions: introducing the gamma correction. Acta Cryst. D53:1997;371-376.
    • (1997) Acta Cryst. , vol.53 , pp. 371-376
    • Abrahams, J.P.1
  • 2
    • 0030038464 scopus 로고    scopus 로고
    • Methods used in the structure determination of bovine mitochondrial F1 ATPase
    • Abrahams J.P., Leslie A.G.W. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst. D52:(Part 1):1996;30-42.
    • (1996) Acta Cryst. , vol.52 , Issue.PART 1 , pp. 30-42
    • Abrahams, J.P.1    Leslie, A.G.W.2
  • 3
    • 0006908476 scopus 로고
    • Method for obtaining a high resolution protein map starting from a low resolution map
    • Agarwal R.C., Isaacs N.W. Method for obtaining a high resolution protein map starting from a low resolution map. Proc. Natl. Acad. Sci. USA. 74:(7):1977;2835-2839.
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , Issue.7 , pp. 2835-2839
    • Agarwal, R.C.1    Isaacs, N.W.2
  • 4
    • 0001478871 scopus 로고
    • PRISM: Topologically constrained phase refinement for macromolecular crystallography
    • Baker D., Bystroff C., Fletterick R.J., Agard D.A. PRISM: Topologically constrained phase refinement for macromolecular crystallography. Acta Cryst. D49:1993;429-439.
    • (1993) Acta Cryst. , vol.49 , pp. 429-439
    • Baker, D.1    Bystroff, C.2    Fletterick, R.J.3    Agard, D.A.4
  • 5
    • 0000195345 scopus 로고
    • Geometric redundancy in intensity data and their use for phase determination
    • Bricogne G. Geometric redundancy in intensity data and their use for phase determination. Acta Cryst. A30:1974;395-405.
    • (1974) Acta Cryst. , vol.30 , pp. 395-405
    • Bricogne, G.1
  • 6
    • 84944818743 scopus 로고
    • Methods and programs for direct-space exploitation of geometric redundancies
    • Bricogne G. Methods and programs for direct-space exploitation of geometric redundancies. Acta Cryst. A32:1976;832-847.
    • (1976) Acta Cryst. , vol.32 , pp. 832-847
    • Bricogne, G.1
  • 7
    • 0026597444 scopus 로고
    • Free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992;472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 8
    • 0013513432 scopus 로고    scopus 로고
    • Introduction to the use of non-crystallographic symmetry in phasing
    • S. Fortier. Dordrecht/Boston/London: Kluwer Academic Publishers
    • Chapman M.S. Introduction to the use of non-crystallographic symmetry in phasing. Fortier S. Direct Methods for Solving Macromolecular Structures. 1998;99-108 Kluwer Academic Publishers, Dordrecht/Boston/London.
    • (1998) Direct Methods for Solving Macromolecular Structures , pp. 99-108
    • Chapman, M.S.1
  • 9
    • 0033198415 scopus 로고    scopus 로고
    • Error estimation and bias correction in phase improvement calculations
    • in press
    • Cowtan, K.D., 1999. Error estimation and bias correction in phase improvement calculations. Acta Cryst D, in press.
    • (1999) Acta Cryst D
    • Cowtan, K.D.1
  • 10
    • 0002473587 scopus 로고    scopus 로고
    • Phase combination and cross validation in iterated density modification calculations
    • Cowtan K.D., Main P. Phase combination and cross validation in iterated density modification calculations. Acta Cryst. D52:1996;43-48.
    • (1996) Acta Cryst. , vol.52 , pp. 43-48
    • Cowtan, K.D.1    Main, P.2
  • 11
    • 0032128419 scopus 로고    scopus 로고
    • Miscellaneous algorithms for density modification
    • Cowtan K.D., Main P. Miscellaneous algorithms for density modification. Acta Cryst. D54:1998;487-493.
    • (1998) Acta Cryst. , vol.54 , pp. 487-493
    • Cowtan, K.D.1    Main, P.2
  • 12
    • 84944813643 scopus 로고
    • On the application of phase relationships to complex structures. XXII. Techniques for random phase refinement
    • Debaerdemaeker T., Woolfson M.M. On the application of phase relationships to complex structures. XXII. Techniques for random phase refinement. Acta Cryst. A39:1983;193-196.
    • (1983) Acta Cryst. , vol.39 , pp. 193-196
    • Debaerdemaeker, T.1    Woolfson, M.M.2
  • 13
    • 0022307513 scopus 로고
    • Computer skeletonization and automatic electron-density map analysis
    • H.W. Wyckoff, C.H.W. Hirs, Timasheff S.N. Orlando: Academic Press
    • Greer J. Computer skeletonization and automatic electron-density map analysis. Wyckoff H.W., Hirs C.H.W., Timasheff S.N. Diffraction Methods for Biological Macromolecules. Vol. 115:1985;206-224 Academic Press, Orlando.
    • (1985) Diffraction Methods for Biological Macromolecules , vol.115 , pp. 206-224
    • Greer, J.1
  • 14
    • 0030503194 scopus 로고    scopus 로고
    • Direct-space methods in phase extension and phase refinement. V. The histogram moments method
    • Gu Y.X., Woolfson M.M., Yao J.X. Direct-space methods in phase extension and phase refinement. V. The histogram moments method. Acta Cryst. D52:(Part 6):1996;1114-1118.
    • (1996) Acta Cryst. , vol.52 , Issue.PART 6 , pp. 1114-1118
    • Gu, Y.X.1    Woolfson, M.M.2    Yao, J.X.3
  • 15
    • 84972193720 scopus 로고
    • Histogram specification as a method of density modification
    • Harrison R.W. Histogram specification as a method of density modification. Appl. Cryst. 21:1988;949-952.
    • (1988) Appl. Cryst. , vol.21 , pp. 949-952
    • Harrison, R.W.1
  • 16
    • 0022749569 scopus 로고
    • The direct methods of X-ray crystallography
    • Hauptman H. The direct methods of X-ray crystallography. Science. 233:1986;178-183.
    • (1986) Science , vol.233 , pp. 178-183
    • Hauptman, H.1
  • 17
    • 0001804798 scopus 로고
    • Phasing methods for protein crystallography
    • D. Moras, A.D. Podjarny, & J.C. Thierry. Oxford: Oxford University Press
    • Hauptman H. Phasing methods for protein crystallography. Moras D., Podjarny A.D., Thierry J.C. Crystallographic Computing 5: From Chemistry to Biology. 1991;324-332 Oxford University Press, Oxford.
    • (1991) Crystallographic Computing 5: From Chemistry to Biology , pp. 324-332
    • Hauptman, H.1
  • 18
    • 0030783379 scopus 로고    scopus 로고
    • A minimal principle in the phase problem
    • Hauptman H. A minimal principle in the phase problem. Current Opinion in Structural Biology. 7:(5):1997;672-680.
    • (1997) Current Opinion in Structural Biology , vol.7 , Issue.5 , pp. 672-680
    • Hauptman, H.1
  • 19
    • 0000980729 scopus 로고
    • Representation of phase probability distributions for simplified combination of independent phase information
    • Hendrickson W.A., Lattman E.E. representation of phase probability distributions for simplified combination of independent phase information. Acta Cryst. B26:1970;136-143.
    • (1970) Acta Cryst. , vol.26 , pp. 136-143
    • Hendrickson, W.A.1    Lattman, E.E.2
  • 20
    • 0013191662 scopus 로고
    • Phase correction, a new method to solve partially known structures
    • Hoppe W., Gassmann J. Phase correction, a new method to solve partially known structures. Acta Cryst. B24:1968;97-107.
    • (1968) Acta Cryst. , vol.24 , pp. 97-107
    • Hoppe, W.1    Gassmann, J.2
  • 21
    • 37049186438 scopus 로고
    • Recovering phase information from intensity data
    • Karle J. Recovering phase information from intensity data. Science. 232:1986;837-843.
    • (1986) Science , vol.232 , pp. 837-843
    • Karle, J.1
  • 22
    • 0030852350 scopus 로고    scopus 로고
    • Automated refinement for protein crystallography
    • Lamzin V.S., Wilson K.S. Automated refinement for protein crystallography. Methods in Enzymology. 277:1997;269-305.
    • (1997) Methods in Enzymology , vol.277 , pp. 269-305
    • Lamzin, V.S.1    Wilson, K.S.2
  • 23
    • 84944815706 scopus 로고
    • A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang
    • Leslie A.G.W. A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang. Acta Cryst. A43:1987;134-136.
    • (1987) Acta Cryst. , vol.43 , pp. 134-136
    • Leslie, A.G.W.1
  • 24
    • 0001383204 scopus 로고
    • Use of the information on electron density distribution in macromolecules
    • Lunin V.Y. Use of the information on electron density distribution in macromolecules. Acta Cryst. A44:1988;144-150.
    • (1988) Acta Cryst. , vol.44 , pp. 144-150
    • Lunin, V.Y.1
  • 25
    • 0032168975 scopus 로고    scopus 로고
    • On the ab initio solution of the phase problem for macromolecules at very low resolution. II. generalized likelihood based approach to cluster discrimination
    • Lunin V.Y., Lunina N.L., Petrova T.E., Urzhumtsev A.G., Podjarny A.D. On the ab initio solution of the phase problem for macromolecules at very low resolution. II. generalized likelihood based approach to cluster discrimination. Acta Cryst. D54:1998;726-734.
    • (1998) Acta Cryst. , vol.54 , pp. 726-734
    • Lunin, V.Y.1    Lunina, N.L.2    Petrova, T.E.3    Urzhumtsev, A.G.4    Podjarny, A.D.5
  • 26
    • 0029175753 scopus 로고
    • On the ab initio solution of the phase problem for macromolecules at very low resolution: The few atoms model method
    • Lunin V.Y., Lunina N.L., Petrova T.E., Vernoslova E.A., Urzhumtsev A.G., Podjarny A.D. On the ab initio solution of the phase problem for macromolecules at very low resolution: the few atoms model method. Acta Cryst. D51:1995;896-903.
    • (1995) Acta Cryst. , vol.51 , pp. 896-903
    • Lunin, V.Y.1    Lunina, N.L.2    Petrova, T.E.3    Vernoslova, E.A.4    Urzhumtsev, A.G.5    Podjarny, A.D.6
  • 27
    • 0000247343 scopus 로고
    • Direct low-resolution phasing from electron-density histograms in protein crystallography
    • Lunin V.Y., Urzhumtsev A.G., Skovoroda T.P. Direct low-resolution phasing from electron-density histograms in protein crystallography. Acta Cryst. A46:1990;540-544.
    • (1990) Acta Cryst. , vol.46 , pp. 540-544
    • Lunin, V.Y.1    Urzhumtsev, A.G.2    Skovoroda, T.P.3
  • 28
    • 84945109248 scopus 로고
    • The use of Sayre's Equation with constraints for the direct determination of phases
    • Main P. The use of Sayre's Equation with constraints for the direct determination of phases. Acta Cryst. A46:1990;372-377.
    • (1990) Acta Cryst. , vol.46 , pp. 372-377
    • Main, P.1
  • 29
    • 0027909076 scopus 로고
    • On the application of the minimal principle to solve unknown structures
    • Miller R., DeTitta G.T., Jones R., Langs D.A., Weeks C.M., Hauptman H.A. On the application of the minimal principle to solve unknown structures. Science. 259:(5100):1993;1430-1433.
    • (1993) Science , vol.259 , Issue.5100 , pp. 1430-1433
    • Miller, R.1    Detitta, G.T.2    Jones, R.3    Langs, D.A.4    Weeks, C.M.5    Hauptman, H.A.6
  • 30
    • 84920325457 scopus 로고
    • AMoRe: An automated package for molecular replacement
    • Navaza J. AMoRe: an automated package for molecular replacement. Acta Cryst. A50:1994;157-163.
    • (1994) Acta Cryst. , vol.50 , pp. 157-163
    • Navaza, J.1
  • 31
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42:1986;140-149.
    • (1986) Acta Cryst. , vol.42 , pp. 140-149
    • Read, R.J.1
  • 33
    • 0030047925 scopus 로고    scopus 로고
    • Direct-space methods in phase extension and phase refinement. iv. the double-histogram method
    • Refaat L.S., Tate C., Woolfson M.M. Direct-space methods in phase extension and phase refinement. iv. the double-histogram method. Acta Cryst. D52:1996;252-256.
    • (1996) Acta Cryst. , vol.52 , pp. 252-256
    • Refaat, L.S.1    Tate, C.2    Woolfson, M.M.3
  • 34
    • 0001331319 scopus 로고
    • Direct-space methods in phase extension and phase determination. II. Developments of low-density elimination
    • Refaat L.S., Woolfson M.M. Direct-space methods in phase extension and phase determination. II. Developments of low-density elimination. Acta Cryst. D49:1993;367-371.
    • (1993) Acta Cryst. , vol.49 , pp. 367-371
    • Refaat, L.S.1    Woolfson, M.M.2
  • 35
    • 0029188074 scopus 로고
    • Phase improvement by cross-validated density modification
    • Roberts A.L.U., Brünger A.T. Phase improvement by cross-validated density modification. Acta Cryst. D51:1995;990-1002.
    • (1995) Acta Cryst. , vol.51 , pp. 990-1002
    • Roberts, A.L.U.1    Brünger, A.T.2
  • 37
    • 25744444396 scopus 로고
    • Least-squares phase refinement. II. high-resolution phasing of a small protein
    • Sayre D. Least-squares phase refinement. II. high-resolution phasing of a small protein. Acta Cryst. A30:1974;180-184.
    • (1974) Acta Cryst. , vol.30 , pp. 180-184
    • Sayre, D.1
  • 38
    • 0001620026 scopus 로고    scopus 로고
    • MAGICSQUASH - More Versatile Non-Crystallographic Averaging With Multiple Constraints
    • Schuller D.J. MAGICSQUASH - More Versatile Non-Crystallographic Averaging With Multiple Constraints. Acta Cryst. D52:(Part 3):1996;425-434.
    • (1996) Acta Cryst. , vol.52 , Issue.PART 3 , pp. 425-434
    • Schuller, D.J.1
  • 39
    • 0000446384 scopus 로고
    • Determination and restrained least-squares refinement of the crystal structures of ribonuclease Sa and its complex with 3′guanylic acid at 1.8A resolution
    • Sevcik J., Dodson E., Dodson G.G. Determination and restrained least-squares refinement of the crystal structures of ribonuclease Sa and its complex with 3′guanylic acid at 1.8A resolution. Acta Cryst. B47:1991;240-253.
    • (1991) Acta Cryst. , vol.47 , pp. 240-253
    • Sevcik, J.1    Dodson, E.2    Dodson, G.G.3
  • 40
    • 37549022003 scopus 로고
    • Structure solution by iterative peaklist optimization and tangent expansion in space group P1
    • Sheldrick G.M., Gould R.O. Structure solution by iterative peaklist optimization and tangent expansion in space group P1. Acta Cryst. B51:1995;423-431.
    • (1995) Acta Cryst. , vol.51 , pp. 423-431
    • Sheldrick, G.M.1    Gould, R.O.2
  • 41
    • 0000164425 scopus 로고
    • Direct-space methods in phase extension and phase determination. I. Low-density elimination
    • Shiono M., Woolfson M.M. Direct-space methods in phase extension and phase determination. I. Low-density elimination. Acta Cryst. A48:1992;451-456.
    • (1992) Acta Cryst. , vol.48 , pp. 451-456
    • Shiono, M.1    Woolfson, M.M.2
  • 42
    • 0000739975 scopus 로고
    • The distribution of phase angles for structures containing heavy atoms. II. A modification of the normal heavy-atom method for non-centrosymmetrical structures
    • Sim G.A. The distribution of phase angles for structures containing heavy atoms. II. A modification of the normal heavy-atom method for non-centrosymmetrical structures. Acta Cryst. 12:1959;813-815.
    • (1959) Acta Cryst. , vol.12 , pp. 813-815
    • Sim, G.A.1
  • 43
    • 0000136206 scopus 로고
    • Core tracing: Depicting connections between features in electron density
    • Swanson S.M. Core tracing: depicting connections between features in electron density. Acta Cryst. D50:1994;695-708.
    • (1994) Acta Cryst. , vol.50 , pp. 695-708
    • Swanson, S.M.1
  • 44
    • 0001280470 scopus 로고
    • DEMON/ANGEL: A suite of programs to carry out density modification
    • Vellieux F.M.D., Hunt J.F., Roy S., Read R.J. DEMON/ANGEL: a suite of programs to carry out density modification. J. Appl. Cryst. 28:1995;347-351.
    • (1995) J. Appl. Cryst. , vol.28 , pp. 347-351
    • Vellieux, F.M.D.1    Hunt, J.F.2    Roy, S.3    Read, R.J.4
  • 45
    • 0022325950 scopus 로고
    • Resolution of phase ambiguity in macromolecular crystallography
    • H.W. Wyckoff, C.H.W. Hirs, Timasheff S.N. Orlando: Academic Press
    • Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Wyckoff H.W., Hirs C.H.W., Timasheff S.N. Diffraction Methods for Biological Macromolecules. Vol. 115:1985;90-113 Academic Press, Orlando.
    • (1985) Diffraction Methods for Biological Macromolecules , vol.115 , pp. 90-113
    • Wang, B.C.1
  • 48
    • 0001210234 scopus 로고
    • The probability distribution of x-ray intensities
    • Wilson A.J.C. The probability distribution of x-ray intensities. Acta Cryst. 2:1949;318-321.
    • (1949) Acta Cryst. , vol.2 , pp. 318-321
    • Wilson, A.J.C.1
  • 49
    • 0001503928 scopus 로고
    • Direct methods - From birth to maturity
    • Woolfson M.M. Direct methods - from birth to maturity. Acta Cryst. A43:1987;593-612.
    • (1987) Acta Cryst. , vol.43 , pp. 593-612
    • Woolfson, M.M.1
  • 50
    • 0000858864 scopus 로고
    • SQUASH - combining constraints for macromolecular phase refinement and extension
    • Zhang K.Y.J. SQUASH - combining constraints for macromolecular phase refinement and extension. Acta Cryst. D49:1993;213-222.
    • (1993) Acta Cryst. , vol.49 , pp. 213-222
    • Zhang, K.Y.J.1
  • 51
    • 0030817618 scopus 로고    scopus 로고
    • Combining constraints for electron density modification
    • C.W. Carter, Sweet R.M. New york: Academic Press
    • Zhang K.Y.J., Cowtan K.D., Main P. Combining constraints for electron density modification. Carter C.W., Sweet R.M. Macromolecular Crystallography. Vol. 277:1997;53-64 Academic Press, New york.
    • (1997) Macromolecular Crystallography , vol.277 , pp. 53-64
    • Zhang, K.Y.J.1    Cowtan, K.D.2    Main, P.3
  • 52
    • 84944812185 scopus 로고
    • Histogram matching as a new density modification technique for phase refinement and extension of protein molecules
    • Zhang K.Y.J., Main P. Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A46:1990;41-46.
    • (1990) Acta Cryst. , vol.46 , pp. 41-46
    • Zhang, K.Y.J.1    Main, P.2
  • 53
    • 84945092441 scopus 로고
    • The use of Sayre's Equation with solvent flattening and histogram matching for phase extension and refinement of protein structures
    • Zhang K.Y.J., Main P. The use of Sayre's Equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Cryst. A46:1990;377-381.
    • (1990) Acta Cryst. , vol.46 , pp. 377-381
    • Zhang, K.Y.J.1    Main, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.