-
1
-
-
0027918556
-
-
M. Levitt and B H Park, Structure 1, 223 (1993); E. Westhof, Water and Biological Macromolecules (CRC Press, Boca Raton, FL. 1993), B T. Nall and K A Dill, Conformations and Forces in Protein Folding (American Association for the Advancement of Science, Washington, DC. 1991)
-
(1993)
Structure
, vol.1
, pp. 223
-
-
Levitt, M.1
Park, B.H.2
-
2
-
-
0027918556
-
-
CRC Press, Boca Raton, FL
-
M. Levitt and B H Park, Structure 1, 223 (1993); E. Westhof, Water and Biological Macromolecules (CRC Press, Boca Raton, FL. 1993), B T. Nall and K A Dill, Conformations and Forces in Protein Folding (American Association for the Advancement of Science, Washington, DC. 1991)
-
(1993)
Water and Biological Macromolecules
-
-
Westhof, E.1
-
3
-
-
0027918556
-
-
American Association for the Advancement of Science, Washington, DC
-
M. Levitt and B H Park, Structure 1, 223 (1993); E. Westhof, Water and Biological Macromolecules (CRC Press, Boca Raton, FL. 1993), B T. Nall and K A Dill, Conformations and Forces in Protein Folding (American Association for the Advancement of Science, Washington, DC. 1991)
-
(1991)
Conformations and Forces in Protein Folding
-
-
Nall, B.T.1
Dill, K.A.2
-
4
-
-
85013546157
-
-
W S Bennett and R Huber, Crit Rev. Biochem. 15, 291 (1985), G. E Schulz, Curr. Opin Struct Biol. 1, 883 (1991), M Gerstein, A Lesk, C. Chothia, Biochemistry 33, 6739 (1994)
-
(1985)
Crit Rev. Biochem.
, vol.15
, pp. 291
-
-
Bennett, W.S.1
Huber, R.2
-
5
-
-
0000453761
-
-
W S Bennett and R Huber, Crit Rev. Biochem. 15, 291 (1985), G. E Schulz, Curr. Opin Struct Biol. 1, 883 (1991), M Gerstein, A Lesk, C. Chothia, Biochemistry 33, 6739 (1994)
-
(1991)
Curr. Opin Struct Biol.
, vol.1
, pp. 883
-
-
Schulz, G.E.1
-
6
-
-
0028335096
-
-
W S Bennett and R Huber, Crit Rev. Biochem. 15, 291 (1985), G. E Schulz, Curr. Opin Struct Biol. 1, 883 (1991), M Gerstein, A Lesk, C. Chothia, Biochemistry 33, 6739 (1994)
-
(1994)
Biochemistry
, vol.33
, pp. 6739
-
-
Gerstein, M.1
Lesk, A.2
Chothia, C.3
-
9
-
-
0028964325
-
-
J. Badger and D L D Caspar, Proc Natl. Acad Sci. U S.A 88, 622 (1991): J. Badger et al , Nature Struct Biol. 2, 77 (1995).
-
(1995)
Nature Struct Biol.
, vol.2
, pp. 77
-
-
Badger, J.1
-
11
-
-
0023053635
-
-
J. Kuriyan et al , ibid. 190, 227 (1986); T Ichiye and M Karplus, Proteins Struct. Funct. Genet. 2, 236 (1987), Biochemistry 27, 3487 (1988); W Doster et al , Nature 337, 754 (1989), T. D. Romo et al , Proteins Struct. Funct. Genet 22, 311 (1995)
-
(1986)
J Mol Biol.
, vol.190
, pp. 227
-
-
Kuriyan, J.1
-
12
-
-
0023512803
-
-
J. Kuriyan et al , ibid. 190, 227 (1986); T Ichiye and M Karplus, Proteins Struct. Funct. Genet. 2, 236 (1987), Biochemistry 27, 3487 (1988); W Doster et al , Nature 337, 754 (1989), T. D. Romo et al , Proteins Struct. Funct. Genet 22, 311 (1995)
-
(1987)
Proteins Struct. Funct. Genet.
, vol.2
, pp. 236
-
-
Ichiye, T.1
Karplus, M.2
-
13
-
-
0024276807
-
-
J. Kuriyan et al , ibid. 190, 227 (1986); T Ichiye and M Karplus, Proteins Struct. Funct. Genet. 2, 236 (1987), Biochemistry 27, 3487 (1988); W Doster et al , Nature 337, 754 (1989), T. D. Romo et al , Proteins Struct. Funct. Genet 22, 311 (1995)
-
(1988)
Biochemistry
, vol.27
, pp. 3487
-
-
-
14
-
-
0024976853
-
-
J. Kuriyan et al , ibid. 190, 227 (1986); T Ichiye and M Karplus, Proteins Struct. Funct. Genet. 2, 236 (1987), Biochemistry 27, 3487 (1988); W Doster et al , Nature 337, 754 (1989), T. D. Romo et al , Proteins Struct. Funct. Genet 22, 311 (1995)
-
(1989)
Nature
, vol.337
, pp. 754
-
-
Doster, W.1
-
15
-
-
0029113863
-
-
J. Kuriyan et al , ibid. 190, 227 (1986); T Ichiye and M Karplus, Proteins Struct. Funct. Genet. 2, 236 (1987), Biochemistry 27, 3487 (1988); W Doster et al , Nature 337, 754 (1989), T. D. Romo et al , Proteins Struct. Funct. Genet 22, 311 (1995)
-
(1995)
Proteins Struct. Funct. Genet
, vol.22
, pp. 311
-
-
Romo, T.D.1
-
21
-
-
13344284779
-
-
note
-
III edge, (iii) The dimer forms the asymmetric unit of the crystal (11, 18) providing two independent views of the protein in the crystal lattice
-
-
-
-
22
-
-
0002452464
-
-
Warrington. UK. 29 and 30 January 1993, L. Sawyer, N. Isaacs, S. Bailey, Eds. SERC Daresbury Laboratory, Wamngton, UK
-
4, a high-energy remote wavelength, corresponding to a near maximal value of Δf ′ Complete diffraction data were obtained from a single orientation by offsetting a major axis of the crystal from the spindle (to avoid a blind region) and collecting 65 consecutive 1 5° oscillation images Each 1.5° sector of reciprocal space was measured at spindle settings φ and φ - 180°, to collect Bijvoet mates at one wavelength, and repeated for each wavelength, so that eight images from each region were measured consecutively The same region of reciprocal space was measured at different wavelengths during the same fill on the synchrotron ring to avoid potential systematic errors due to recalibration of the monochromator. Fuji imaging plates were scanned on a Fuji BAS2000 scanner Profile-fit, Lorentz polarization-corrected intensities were obtained with the use of DENZO and SCALEPACK [Z Otwinowski. Proceedings of the CCP4 Study Weekend Data Collection and Processing Warrington. UK. 29 and 30 January 1993, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Wamngton, UK, 1993), pp. 56-62]. Bijvoet mates were treated as independent observations for scaling and merging Diffraction data for the four wavelengths were placed on a quasi-absolute scale, and the four data sets were scaled to one another with the CCP4 programs TRUNCATE and RSTATS [Collaborative Computing Project 4, The CCP4 Suite: Programs for Protein Crystallography (SERC Daresbury Laboratory, Wamngton, UK, 1994)] for the MADLSQ calculations, and with X-PLOR (27) for the probabilistic calculations
-
(1993)
Proceedings of the CCP4 Study Weekend Data Collection and Processing
, pp. 56-62
-
-
Otwinowski, Z.1
-
23
-
-
4243126064
-
-
SERC Daresbury Laboratory, Wamngton, UK
-
4, a high-energy remote wavelength, corresponding to a near maximal value of Δf ′ Complete diffraction data were obtained from a single orientation by offsetting a major axis of the crystal from the spindle (to avoid a blind region) and collecting 65 consecutive 1 5° oscillation images Each 1.5° sector of reciprocal space was measured at spindle settings φ and φ - 180°, to collect Bijvoet mates at one wavelength, and repeated for each wavelength, so that eight images from each region were measured consecutively The same region of reciprocal space was measured at different wavelengths during the same fill on the synchrotron ring to avoid potential systematic errors due to recalibration of the monochromator. Fuji imaging plates were scanned on a Fuji BAS2000 scanner Profile-fit, Lorentz polarization-corrected intensities were obtained with the use of DENZO and SCALEPACK [Z Otwinowski. Proceedings of the CCP4 Study Weekend Data Collection and Processing Warrington. UK. 29 and 30 January 1993, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Wamngton, UK, 1993), pp. 56-62]. Bijvoet mates were treated as independent observations for scaling and merging Diffraction data for the four wavelengths were placed on a quasi-absolute scale, and the four data sets were scaled to one another with the CCP4 programs TRUNCATE and RSTATS [Collaborative Computing Project 4, The CCP4 Suite: Programs for Protein Crystallography (SERC Daresbury Laboratory, Wamngton, UK, 1994)] for the MADLSQ calculations, and with X-PLOR (27) for the probabilistic calculations
-
(1994)
The CCP4 Suite: Programs for Protein Crystallography
-
-
-
25
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13344281167
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note
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Anisotropic scale factors were applied to the unmerged diffraction data to reduce noise in the Bijvoet and dispersive differences. The MADLSQ procedure was applied to the scaled and unmerged diffraction data Redundantly determined amplitudes and phases were merged after the MADLSQ procedure (10).
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-
-
-
27
-
-
0000019861
-
-
2dφ (4) [G Bricogne, Acta Crystallogr. A40, 410 (1984); Z. Otwinowski, Proceedings of the CCP4 Study Weekend, Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991, pp 80-85]. This method is similar to the generation of phase probability distributions from the MADLSQ-derived wavelength-independent structure factors by the MADABCD procedure (16), in that Bijvoet and dispersive differences contribute to a lack-of-closure expression for each measured data point.
-
(1980)
Acta Crystallogr
, vol.A36
, pp. 856
-
-
Phillips, J.C.1
Hodgson, K.O.2
-
28
-
-
0002016798
-
-
2dφ (4) [G Bricogne, Acta Crystallogr. A40, 410 (1984); Z. Otwinowski, Proceedings of the CCP4 Study Weekend, Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991, pp 80-85]. This method is similar to the generation of phase probability distributions from the MADLSQ-derived wavelength-independent structure factors by the MADABCD procedure (16), in that Bijvoet and dispersive differences contribute to a lack-of-closure expression for each measured data point.
-
(1987)
Acta Crystallogr.
, vol.A43
, pp. 6
-
-
Terwilliger, T.C.1
Eisenberg, D.2
-
29
-
-
0027402969
-
-
2dφ (4) [G Bricogne, Acta Crystallogr. A40, 410 (1984); Z. Otwinowski, Proceedings of the CCP4 Study Weekend, Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991, pp 80-85]. This method is similar to the generation of phase probability distributions from the MADLSQ-derived wavelength-independent structure factors by the MADABCD procedure (16), in that Bijvoet and dispersive differences contribute to a lack-of-closure expression for each measured data point.
-
(1993)
Nature
, vol.362
, pp. 219
-
-
Ramakrishnan, V.1
Finch, J.T.2
Graziano, V.3
Lee, P.L.4
Sweet, R.M.5
-
30
-
-
13344284778
-
-
in preparation
-
2dφ (4) [G Bricogne, Acta Crystallogr. A40, 410 (1984); Z. Otwinowski, Proceedings of the CCP4 Study Weekend, Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991, pp 80-85]. This method is similar to the generation of phase probability distributions from the MADLSQ-derived wavelength-independent structure factors by the MADABCD procedure (16), in that Bijvoet and dispersive differences contribute to a lack-of-closure expression for each measured data point.
-
-
-
Brünger, A.T.1
Flaherty, K.M.2
Burling, F.T.3
Weis, W.I.4
-
31
-
-
84944818276
-
-
2dφ (4) [G Bricogne, Acta Crystallogr. A40, 410 (1984); Z. Otwinowski, Proceedings of the CCP4 Study Weekend, Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991, pp 80-85]. This method is similar to the generation of phase probability distributions from the MADLSQ-derived wavelength-independent structure factors by the MADABCD procedure (16), in that Bijvoet and dispersive differences contribute to a lack-of-closure expression for each measured data point.
-
(1984)
Acta Crystallogr.
, vol.A40
, pp. 410
-
-
Bricogne, G.1
-
32
-
-
0002634621
-
-
Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. SERC Daresbury Laboratory, Warrington, UK
-
2dφ (4) [G Bricogne, Acta Crystallogr. A40, 410 (1984); Z. Otwinowski, Proceedings of the CCP4 Study Weekend, Warrington, UK, 25 and 26 January 1991, W. Wolf, P. R. Evans, A. G. W. Leslie, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1991, pp 80-85]. This method is similar to the generation of phase probability distributions from the MADLSQ-derived wavelength-independent structure factors by the MADABCD procedure (16), in that Bijvoet and dispersive differences contribute to a lack-of-closure expression for each measured data point.
-
(1991)
Proceedings of the CCP4 Study Weekend
, pp. 80-85
-
-
Otwinowski, Z.1
-
33
-
-
0026342025
-
-
W. I. Weis, R Kahn, R. Fourme, K Drickamer, W. A. Hendrickson, Science 254, 1608 (1991)
-
(1991)
Science
, vol.254
, pp. 1608
-
-
Weis, W.I.1
Kahn, R.2
Fourme, R.3
Drickamer, K.4
Hendrickson, W.A.5
-
35
-
-
13344280460
-
-
unpublished data
-
217 sulfhydryl group was refined with two alternative conformations (Fig. 1B) All refinements were performed with X-PLOR (27)
-
-
-
Weis, W.I.1
-
37
-
-
79952608525
-
-
217 sulfhydryl group was refined with two alternative conformations (Fig. 1B) All refinements were performed with X-PLOR (27)
-
(1991)
Acta Crystallogr.
, vol.A47
, pp. 392
-
-
Engh, R.A.1
Huber, R.2
-
38
-
-
0026464832
-
-
W I. Weis, K Drickamer, W. A. Hendrickson,Nature 360, 127 (1992), W I Weis and K Drickamer, Structure 2, 1227 (1994).
-
(1992)
Nature
, vol.360
, pp. 127
-
-
Weis, W.I.1
Drickamer, K.2
Hendrickson, W.A.3
-
39
-
-
0028774718
-
-
W I. Weis, K Drickamer, W. A. Hendrickson,Nature 360, 127 (1992), W I Weis and K Drickamer, Structure 2, 1227 (1994).
-
(1994)
Structure
, vol.2
, pp. 1227
-
-
Weis, W.I.1
Drickamer, K.2
-
40
-
-
0025943869
-
-
3+ were restrained to their initial positions Conformers of the protein were rendered invisible to each other in terms of chemical interactions Each conformer in the ensemble contributed equally to the calculated structure factor with the occupancy set to the reciprocal of the number of conformers. Evaluation of the free R value as a function of the number of conformers produced a shallow minimum for eight conformers, which were used for subsequent analysis
-
(1991)
Proteins
, vol.10
, pp. 340
-
-
Kuriyan, J.1
-
41
-
-
0003530127
-
-
Springer-Verlag, New York
-
calc) is an approximation of the vector difference map [J. Drenth, Principles of Protein X-ray Crystallography (Springer-Verlag, New York, 1994), pp. 150-152]. As a consequence, vector difference maps of sub-MBP-A were observed to have less noise than conventional difference maps
-
(1994)
Principles of Protein X-ray Crystallography
, pp. 150-152
-
-
Drenth, J.1
-
44
-
-
0024094768
-
-
M. Levitt and R. Sharon, Proc Natl Acad. Sci U.S A. 85, 7557 (1988), Y. Komeiji et al., Proteins 16, 268 (1993); M Karplus and G. A. Petsko, Nature 347, 631 (1990); P. J Steinbach and B. R Brooks, Proc. Natl Acad. Sci. U.S A 90, 9135 (1993); V Lounnas et al., Biophys. J 66, 601 (1994).
-
(1988)
Proc Natl Acad. Sci U.S A.
, vol.85
, pp. 7557
-
-
Levitt, M.1
Sharon, R.2
-
45
-
-
0027211701
-
-
M. Levitt and R. Sharon, Proc Natl Acad. Sci U.S A. 85, 7557 (1988), Y. Komeiji et al., Proteins 16, 268 (1993); M Karplus and G. A. Petsko, Nature 347, 631 (1990); P. J Steinbach and B. R Brooks, Proc. Natl Acad. Sci. U.S A 90, 9135 (1993); V Lounnas et al., Biophys. J 66, 601 (1994).
-
(1993)
Proteins
, vol.16
, pp. 268
-
-
Komeiji, Y.1
-
46
-
-
0025048105
-
-
M. Levitt and R. Sharon, Proc Natl Acad. Sci U.S A. 85, 7557 (1988), Y. Komeiji et al., Proteins 16, 268 (1993); M Karplus and G. A. Petsko, Nature 347, 631 (1990); P. J Steinbach and B. R Brooks, Proc. Natl Acad. Sci. U.S A 90, 9135 (1993); V Lounnas et al., Biophys. J 66, 601 (1994).
-
(1990)
Nature
, vol.347
, pp. 631
-
-
Karplus, M.1
Petsko, G.A.2
-
47
-
-
0027431378
-
-
M. Levitt and R. Sharon, Proc Natl Acad. Sci U.S A. 85, 7557 (1988), Y. Komeiji et al., Proteins 16, 268 (1993); M Karplus and G. A. Petsko, Nature 347, 631 (1990); P. J Steinbach and B. R Brooks, Proc. Natl Acad. Sci. U.S A 90, 9135 (1993); V Lounnas et al., Biophys. J 66, 601 (1994).
-
(1993)
Proc. Natl Acad. Sci. U.S A
, vol.90
, pp. 9135
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
48
-
-
0028218493
-
-
M. Levitt and R. Sharon, Proc Natl Acad. Sci U.S A. 85, 7557 (1988), Y. Komeiji et al., Proteins 16, 268 (1993); M Karplus and G. A. Petsko, Nature 347, 631 (1990); P. J Steinbach and B. R Brooks, Proc. Natl Acad. Sci. U.S A 90, 9135 (1993); V Lounnas et al., Biophys. J 66, 601 (1994).
-
(1994)
Biophys. J
, vol.66
, pp. 601
-
-
Lounnas, V.1
-
49
-
-
4243436882
-
-
D. C Rees and M Lewis, Acta Crystallogr. A39, 94 (1983); E Arnold and M G Rossmann, ibid A44, 270 (1988), L. M. Rice and A. T. Brünger, Proteins Struct. Funct Genet. 19, 277 (1994).
-
(1983)
Acta Crystallogr.
, vol.A39
, pp. 94
-
-
Rees, D.C.1
Lewis, M.2
-
50
-
-
84944816485
-
-
D. C Rees and M Lewis, Acta Crystallogr. A39, 94 (1983); E Arnold and M G Rossmann, ibid A44, 270 (1988), L. M. Rice and A. T. Brünger, Proteins Struct. Funct Genet. 19, 277 (1994).
-
(1988)
Acta Crystallogr.
, vol.A44
, pp. 270
-
-
Arnold, E.1
Rossmann, M.G.2
-
51
-
-
0028070557
-
-
D. C Rees and M Lewis, Acta Crystallogr. A39, 94 (1983); E Arnold and M G Rossmann, ibid A44, 270 (1988), L. M. Rice and A. T. Brünger, Proteins Struct. Funct Genet. 19, 277 (1994).
-
(1994)
Proteins Struct. Funct Genet.
, vol.19
, pp. 277
-
-
Rice, L.M.1
Brünger, A.T.2
-
52
-
-
0003769049
-
-
Yale Univ. Press, New Haven, CT, developmental version of X-PLOR, available on request
-
A. T Brünger, X-PLOR. Version 3.1 A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1992); developmental version of X-PLOR, available on request.
-
(1992)
X-PLOR. Version 3.1 A System for X-ray Crystallography and NMR
-
-
Brünger, A.T.1
-
53
-
-
0001155122
-
-
D. T. Cramer, J. Appl Crystallogr. 16, 437 (1983), _ and D. L. Liberman, J Chem Phys. 53, 1891 (1970).
-
(1983)
J. Appl Crystallogr.
, vol.16
, pp. 437
-
-
Cramer, D.T.1
-
54
-
-
4644289782
-
-
D. T. Cramer, J. Appl Crystallogr. 16, 437 (1983), _ and D. L. Liberman, J Chem Phys. 53, 1891 (1970).
-
(1970)
J Chem Phys.
, vol.53
, pp. 1891
-
-
Liberman, D.L.1
-
56
-
-
0026034685
-
-
L. M Gregoret, S. D. Rader, R. J. Fletterick, F E. Cohen, Proteins Struct Fund Genet. 9, 99 (1991).
-
(1991)
Proteins Struct Fund Genet.
, vol.9
, pp. 99
-
-
Gregoret, L.M.1
Rader, S.D.2
Fletterick, R.J.3
Cohen, F.E.4
-
57
-
-
13344293831
-
-
note
-
We thank P Gros for assistance in designing the X-PLOR crystallographic language for phasing: V Agrawal, S. Shah, and M. Willis for help with data collection; C Ogata for beamline support; and P. Adams, M Gerstein, M. Levitt, and L Rice for critical reading of the manuscript. The coordinates and the diffraction data have been deposited with the Brookhaven Data Bank (accession number 1YTT). Supported by the Howard Hughes Medical Institute (A.T.B), NSF (DIR9021975, A.T.B.), and NIH (GM50565, W I W) W.I W. is a Pew Scholar in the Biomedical Sciences.
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