International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 2.2, pp. 64-74
doi: 10.1107/97809553602060000809

Chapter 2.2. Quality indicators in macromolecular crystallography: definitions and applications

H. M. Einspahra* and M. S. Weissb

aPO Box 6483, Lawrenceville, NJ 08648–0483, United States, and bHelmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Str. 15, D-12489 Berlin, Germany
Correspondence e-mail:  hmeinspahr@yahoo.com

References

Arnberg, L., Hovmöller, S. & Westman, S. (1979). On the significance of `non-significant' reflexions. Acta Cryst. A35, 497–499.
Blow, D. M. (2002). Rearrangement of Cruickshank's formulae for the diffraction-component precision index. Acta Cryst. D58, 792–797.
Blow, D. M. & Crick, F. H. C. (1959). The treatment of errors in the isomorphous replacement method. Acta Cryst. 12, 794–802.
Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography. New York: Academic Press.
Brünger, A. T. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (London), 355, 472–475.
Brünger, A. T. (1997). Free R value: cross-validation in crystallography. Methods Enzymol. 277, 366–396.
Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.
Cowtan, K. (1999). Error estimation and bias correction in phase-improvement calculations. Acta Cryst. D55, 1555–1567.
Cowtan, K. & Main, P. (1998). Miscellaneous algorithms for density modification. Acta Cryst. D54, 487–493.
Cowtan, K. D. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Cryst. D52, 43–48.
Cruickshank, D. W. J. (1999a). Remarks about protein structure precision. Acta Cryst. D55, 583–601.
Cruickshank, D. W. J. (1999b). Remarks about protein structure precision. Erratum. Acta Cryst. D55, 1108.
Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). The structure of haemoglobin. VIII. A three-dimensional Fourier synthesis at 5.5 Å resolution: determination of the phase angles. Proc. R. Soc. London Ser. A, 265, 15–38.
Diederichs, K. (2006). Some aspects of quantitative analysis and correction of radiation damage. Acta Cryst. D62, 96–101.
Diederichs, K. (2010). Quantifying instrument errors in macromolecular X-ray data sets. Acta Cryst. D66, 733–740.
Diederichs, K. & Karplus, P. A. (1997a). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat. Struct. Biol. 4, 269–275.
Diederichs, K. & Karplus, P. A. (1997b). Improved R-factors for diffraction data analysis in macromolecular crystallography. Erratum. Nat. Struct. Biol. 4, 592.
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A47, 392–400.
Evans, P. (2006). Scaling and assessment of data quality. Acta Cryst. D62, 72–82.
Fisher, S. J., Helliwell, J. R., Khurshid, S., Govada, L., Redwood, C., Squire, J. M. & Chayen, N. E. (2008). An investigation into the protonation states of the C1 domain of cardiac myosin-binding protein C. Acta Cryst. D64, 658–664.
Grosse-Kunstleve, R. W. & Adams, P. D. (2003). Substructure search procedures for macromolecular structures. Acta Cryst. D59, 1966–1973.
Hauptman, H. & Karle, J. (1953). Solution of the phase problem. I. The centrosymmetric crystal. Am. Crystallogr. Assoc. Monograph No. 3. Dayton, Ohio: Polycrystal Book Service.
Hirshfeld, F. L. & Rabinovich, D. (1973). Treating weak reflexions in least-squares calculations. Acta Cryst. A29, 510–513.
Hooft, R. W. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Errors in protein structures. Nature (London), 381, 272.
Howell, P. L. & Smith, G. D. (1992). Identification of heavy-atom derivatives by normal probability methods. J. Appl. Cryst. 25, 81–86.
James, R. W. (1948). False detail in three-dimensional Fourier representations of crystal structures. Acta Cryst. 1, 132–134.
Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110–119.
Kabsch, W. (1988). Evaluation of single-crystal X-ray diffraction data from a position-sensitve detector. J. Appl. Cryst. 21, 916–924.
Kabsch, W. (1993). Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800.
Kabsch, W. (2010). XDS. Acta Cryst. D66, 125–132.
Kleywegt, G. & Brünger, A. T. (1996). Checking your imagination: applications of the free R value. Structure, 4, 897–904.
Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. (2008). BALBES: a molecular-replacement pipeline. Acta Cryst. D64, 125–132.
Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802–810.
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). Phaser crystallographic software. J. Appl. Cryst. 40, 658–674.
Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491–497.
Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326.
Panjikar, S. & Tucker, P. A. (2002). Phasing possibilities using different wavelengths with a xenon derivative. J. Appl. Cryst. 35, 261–266.
Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Cryst. D52, 57–64.
Pflugrath, J. W. (1999). The finer things in X-ray diffraction data collection. Acta Cryst. D55, 1718–1725.
Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42, 140–149.
Read, R. J. (2001). Pushing the boundaries of molecular replacement with maximum likelihood. Acta Cryst. D57, 1373–1382.
Rodgers, J. L. & Nicewander, W. A. (1988). Thirteen ways to look at the correlation coefficient. Am. Stat. 42, 59–66.
Rodriguez, D. D., Grosse, C., Himmel, S., Gonzalez, C., de Ilarduya, I. M., Becker, S., Sheldrick, G. M. & Uson, I. (2009). Crystallographic ab initio protein structure solution below atomic resolution. Nat. Methods, 6, 651–653.
Rossmann, M. G. & Blow, D. M. (1962). The detection of sub-units within the crystallographic asymmetric unit. Acta Cryst. 15, 24–31.
Schneider, T. R. & Sheldrick, G. M. (2002). Substructure solution with SHELXD. Acta Cryst. D58, 1772–1779.
Sheldrick, G. M. (2002). Macromolecular phasing with SHELXE. Z. Kristallogr. 217, 644–650.
Sheldrick, G. M. (2008). A short history of SHELX. Acta Cryst. A64, 112–122.
Sheldrick, G. M. (2010). Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Cryst. D66, 479–485.
Stenkamp, R. E. & Jensen, L. H. (1984). Resolution revisited: limit of detail in electron density maps. Acta Cryst. A40, 251–254.
Terwilliger, T. C. (2001). Map-likelihood phasing. Acta Cryst. D57, 1763–1775.
Terwilliger, T. C., Adams, P. D., Read, R. J., McCoy, A. J., Moriarty, N. W., Grosse-Kunstleve, R. W., Afonine, P. V., Zwart, P. H. & Hung, L.-W. (2009). Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Cryst. D65, 582–601.
Terwilliger, T. C. & Berendzen, J. (1999). Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods. Acta Cryst. D55, 501–505.
Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Cryst. D55, 191–205.
Vellieux, F. M. D. A. P., Hunt, J. F., Roy, S. & Read, R. J. (1995). DEMON/ANGEL: a suite of programs to carry out density modification. J. Appl. Cryst. 28, 347–351.
Weeks, C. M., De Titta, G. T., Miller, R. & Hauptman, H. A. (1993). Application of the minimal principle to peptide structures. Acta Cryst. D49, 179–181.
Weeks, C. M., DeTitta, G. T., Hauptman, H. A., Thuman, P. & Miller, R. (1994). Structure solution by minimal-function phase refinement and Fourier filtering. II. Implementation and applications. Acta Cryst. A50, 210–220.
Weiss, M. S. (2001). Global indicators of X-ray data quality. J. Appl. Cryst. 34, 130–135.
Weiss, M. S. & Hilgenfeld, R. (1997). On the use of the merging R factor as a quality indicator for X-ray data. J. Appl. Cryst. 30, 203–205.
Wilson, A. J. C. (1949). The probability distribution of X-ray intensities. Acta Cryst. 2, 318–321.