New developments in phase refinement

Current Opinion in Structural Biology

Volumn 8, Issue 5, 1998, Pages 601-605

  Abrahams, Jp ^a   De Graaff, Rag ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; MATHEMATICAL ANALYSIS; METHODOLOGY; PRIORITY JOURNAL; PROBABILITY; PROTEIN STRUCTURE; REVIEW; X RAY CRYSTALLOGRAPHY;

EID: 0031790858     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80151-6     Document Type: Article

References (22)

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2. Vellieux FDM, Read RJ. Non crystallographic symmetry averaging in phase refinement and extension. of special interest Methods Enzymol. 277:1997;18-52 The authors provide a clear explanation of the relationship between the structure factors imposed by noncrystallographic symmetry and disordered solvent.
3. Hauptman HA. Phasing methods for protein crystallography. of special interest Curr Opin Struct Biol. 7:1997;672-680 An excellent review of new developments in direct methods. In particular, the procedure used in the 'Shake 'n' Bake' program is lucidly explained.
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5. Chang CS, Weeks CM, Miller R, Hauptman HA. Incorporating tangent refinement in the shake and bake formalism. of special interest Acta Crystallogr A. 53:1997;436-444 The relative merits of tangent refinement and the minimization of the R(φ) function are discussed. Tangent refinement can be more efficient for solving small structures, but the minimization of R(φ) is preferable for larger structures.
6. Weeks CM, De Titta GT, Hauptman HA, Thuman P, Miller R. Structure solution by minimal-function phase refinement and Fourier filtering II. Implementation and applications. Acta Crystallogr A. 50:1994;210-220.
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8. Karle J, Hauptman HA. The phases and magnitudes of structure factors. Acta Crystallogr. 3:1950;181-187.
9. Tsoucaris G. A new method for phase determination: the maximum determinant rule. Acta Crystallogr A. 26:1970;492-499.
10. Heinerman JJL, Kroon J, Krabbendam H. Conditional phase probability distributions of structure factors in a Karle-Hauptman matrix. Acta Crystallogr A. 35:1979;105-107.
11. de Gelder R, de Graaff RAG, Schenk H. Automatic determination of crystal structures using Karle-Hauptman matrices. Acta Crystallogr A. 49:1993;287-293.
12. van der Plas JL, de Graaff RAG, Schenk H. On the use of eigenvalues and eigenvectors in the phase problem. of special interest Acta Crystallogr A. 54:1998;262-266 The authors discuss recent developments in matrix methods. The use of matrices with orders larger than N, the number of atoms in the unit cell, is investigated.
13. van der Plas JL, de Graaff RAG, Schenk H. Karle-Hauptman matrices and eigenvalues: a practical approach. Acta Crystallogr A. 54:1998;267-272.
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16. Wang BC. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115:1985;90-112.
17. Abrahams JP. Bias reduction in phase refinement by modified interference functions: introducing the γ correction. of outstanding interest Acta Crystallogr D. 53:1997;371-376 A general method is described for calculating the magnitude of the bias component in phase refinement. The paper also contains a clear description of the phase relationships introduced by the constraint of solvent flatness.
18. 1 ATPase. Acta Crystallogr D. 52:1996;30-42.
19. De la Fourtelle É, Bricogne G. Maximum-likelihood heavy atom refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. of outstanding interest Methods Enzymol. 276:1997;472-494 The only readily available description of the methods used in SHARP, a program that uses MIR and/or MAD data for phasing.
20. Lamzin VS, Wilson KS. Automated refinement for protein crystallography. of special interest Methods Enzymol. 277:1997;269-305 The authors introduce a method for macromolecular crystallographic phase refinement in which atomicity is introduced automatically, rather than manually through model building.
21. of special interest Perrakis A, Sixma TK, Wilson KS, Lamzin VS. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. of outstanding interest Acta Crystallogr D. 53:1997;448-455 A description of a procedure for phase refinement using multiple automatically generated atomic models. The authors show that the procedure is a significant improvement on the one described in [20].
22. Van Asselt EJ, Perrakis A, Kalk KH, Lamzin VS, Dijkstra BW. Accelerated X-ray structure elucidation of a 36 kDa muraminidase/transglycosylase using wARP. of special interest Acta Crystallogr D. 54:1998;58-73 An elaborated analysis of the wARP procedure.