On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets

Wang, Jimin; Brudvig, Gary W.; Batista, Victor S.; Moore, Peter B.

doi:10.1002/pro.3314

Title: On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets

Abstract

Abstract In 2012, Karplus and Diederichs demonstrated that the Pearson correlation coefficient CC _1/2 is a far better indicator of the quality and resolution of crystallographic data sets than more traditional measures like merging R‐factor or signal‐to‐noise ratio. More specifically, they proposed that CC _1/2 be computed for data sets in thin shells of increasing resolution so that the resolution dependence of that quantity can be examined. Recently, however, the CC _1/2 values of entire data sets, i.e., cumulative correlation coefficients , have been used as a measure of data quality. Here, we show that the difference in cumulative CC _1/2 value between a data set that has been accurately measured and a data set that has not is likely to be small. Furthermore, structures obtained by molecular replacement from poorly measured data sets are likely to suffer from extreme model bias.

Authors:

^[1]; Brudvig, Gary W. ^[2]; Batista, Victor S. ^[3]; Moore, Peter B. ^[2]

Department of Molecular Biophysics and Biochemistry Yale University New Haven Connecticut 06520‐8114
Department of Molecular Biophysics and Biochemistry Yale University New Haven Connecticut 06520‐8114, Department of Chemistry Yale University New Haven Connecticut 06520‐8107
Department of Chemistry Yale University New Haven Connecticut 06520‐8107

Publication Date:: Fri Oct 27 00:00:00 EDT 2017

Sponsoring Org.:: USDOE

OSTI Identifier:: 1405191

Grant/Contract Number:: DESC0001423; DE‐FG0205ER15646

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Protein Science

Additional Journal Information:: Journal Name: Protein Science Journal Volume: 26 Journal Issue: 12; Journal ID: ISSN 0961-8368

Publisher:: Wiley Blackwell (John Wiley & Sons)

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Wang, Jimin, Brudvig, Gary W., Batista, Victor S., and Moore, Peter B. On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets.  United Kingdom: N. p., 2017. 
Web.  doi:10.1002/pro.3314.

Copy to clipboard


                    Wang, Jimin, Brudvig, Gary W., Batista, Victor S., & Moore, Peter B. On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets.  United Kingdom.  https://doi.org/10.1002/pro.3314

Copy to clipboard


                    Wang, Jimin, Brudvig, Gary W., Batista, Victor S., and Moore, Peter B. Fri .  
"On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets".  United Kingdom.  https://doi.org/10.1002/pro.3314.

Copy to clipboard


                    
@article{osti_1405191,

  title        = {On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets},

  author       = {Wang, Jimin and Brudvig, Gary W. and Batista, Victor S. and Moore, Peter B.},

  abstractNote = {Abstract In 2012, Karplus and Diederichs demonstrated that the Pearson correlation coefficient CC 1/2 is a far better indicator of the quality and resolution of crystallographic data sets than more traditional measures like merging R‐factor or signal‐to‐noise ratio. More specifically, they proposed that CC 1/2 be computed for data sets in thin shells of increasing resolution so that the resolution dependence of that quantity can be examined. Recently, however, the CC 1/2 values of entire data sets, i.e., cumulative correlation coefficients , have been used as a measure of data quality. Here, we show that the difference in cumulative CC 1/2 value between a data set that has been accurately measured and a data set that has not is likely to be small. Furthermore, structures obtained by molecular replacement from poorly measured data sets are likely to suffer from extreme model bias.},

  doi          = {10.1002/pro.3314},

  journal      = {Protein Science},

  number       = 12,

  volume       = 26,

  place        = {United Kingdom},

  year         = {Fri Oct 27 00:00:00 EDT 2017},

  month        = {Fri Oct 27 00:00:00 EDT 2017}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (Publisher)

Publisher's Version of Record
https://doi.org/10.1002/pro.3314

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 4 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Linking Crystallographic Model and Data Quality
journal, May 2012

Karplus, P. A.; Diederichs, K.
Science, Vol. 336, Issue 6084
DOI: 10.1126/science.1218231

On the appearance of carboxylates in electrostatic potential maps: ESP Involving Carboxylate Groups
journal, December 2016

Wang, Jimin
Protein Science, Vol. 26, Issue 3
DOI: 10.1002/pro.3093

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures
journal, September 2014

Holton, James M.; Classen, Scott; Frankel, Kenneth A.
The FEBS Journal, Vol. 281, Issue 18
DOI: 10.1111/febs.12922

Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy
journal, October 2003

Rosenthal, Peter B.; Henderson, Richard
Journal of Molecular Biology, Vol. 333, Issue 4
DOI: 10.1016/j.jmb.2003.07.013

Structure of photosystem II and substrate binding at room temperature
journal, November 2016

Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira
Nature, Vol. 540, Issue 7633
DOI: 10.1038/nature20161

The significance of the phase synthesis
journal, May 1961

Srinivasan, R.
Proceedings of the Indian Academy of Sciences - Section A, Vol. 53, Issue 5
DOI: 10.1007/BF03049190

An Apparent Paradox in Crystal Structure Analysis
journal, April 1961

Ramachandran, G. N.; Srinivasan, R.
Nature, Vol. 190, Issue 4771
DOI: 10.1038/190159a0

The probability distribution of X-ray intensities
journal, October 1949

Wilson, A. J. C.
Acta Crystallographica, Vol. 2, Issue 5
DOI: 10.1107/S0365110X49000813

Serial crystallography on in vivo grown microcrystals using synchrotron radiation
journal, February 2014

Gati, Cornelius; Bourenkov, Gleb; Klinge, Marco
IUCrJ, Vol. 1, Issue 2
DOI: 10.1107/S2052252513033939

The mode of attachment of the azide ion to sperm whale metmyoglobin
journal, January 1964

Stryer, L.; Kendrew, J. C.; Watson, H. C.
Journal of Molecular Biology, Vol. 8, Issue 1
DOI: 10.1016/S0022-2836(64)80152-2

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals
journal, June 2012

Kern, J.; Alonso-Mori, R.; Hellmich, J.
Proceedings of the National Academy of Sciences, Vol. 109, Issue 25, p. 9721-9726
DOI: 10.1073/pnas.1204598109

Largest likely values for the reliability index
journal, September 1950

Wilson, A. J. C.
Acta Crystallographica, Vol. 3, Issue 5
DOI: 10.1107/S0365110X50001129

Assessing and maximizing data quality in macromolecular crystallography
journal, October 2015

Karplus, P. Andrew; Diederichs, Kay
Current Opinion in Structural Biology, Vol. 34
DOI: 10.1016/j.sbi.2015.07.003

Identification of rogue datasets in serial crystallography
journal, April 2016

Assmann, Greta; Brehm, Wolfgang; Diederichs, Kay
Journal of Applied Crystallography, Vol. 49, Issue 3
DOI: 10.1107/S1600576716005471

Largest likely values of residuals
journal, November 1974

Wilson, A. J. C.
Acta Crystallographica Section A, Vol. 30, Issue 6
DOI: 10.1107/S0567739474010801

Modeling truncated pixel values of faint reflections in MicroED images
journal, May 2016

Hattne, Johan; Shi, Dan; de la Cruz, M. Jason
Journal of Applied Crystallography, Vol. 49, Issue 3
DOI: 10.1107/S1600576716007196

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.
Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
DOI: 10.1073/pnas.1621152114

Experimental charge density from electron microscopic maps: Laplacian Operation on ESP Maps
journal, May 2017

Wang, Jimin
Protein Science, Vol. 26, Issue 8
DOI: 10.1002/pro.3198

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL
journal, February 2017

Suga, Michihiro; Akita, Fusamichi; Sugahara, Michihiro
Nature, Vol. 543, Issue 7643
DOI: 10.1038/nature21400

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy
journal, July 2014

Kern, Jan; Tran, Rosalie; Alonso-Mori, Roberto
Nature Communications, Vol. 5, Issue 1
DOI: 10.1038/ncomms5371

On the interpretation of electron microscopic maps of biological macromolecules: Electric Potentials Involving Negative Charges
journal, October 2016

Wang, Jimin; Moore, Peter B.
Protein Science, Vol. 26, Issue 1
DOI: 10.1002/pro.3060

New statistical tests for distinguishing between centrosymmetric and non-centrosymmetric structures
journal, November 1966

Srinivasan, R.; Srikrishnan, T.
Acta Crystallographica, Vol. 21, Issue 5
DOI: 10.1107/S0365110X66003645

Why phase errors affect the electron function more than amplitude errors
journal, February 2008

Lattman, Eaton; DeRosier, David
Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 2
DOI: 10.1107/S0108767307067372

Serial crystallography using synchrotron radiation
journal, February 2014

Rossmann, Michael G.
IUCrJ, Vol. 1, Issue 2
DOI: 10.1107/S2052252514000499

Mathematical Contributions to the Theory of Evolution. III. Regression, Heredity, and Panmixia
journal, January 1896

Pearson, K.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 187, Issue 0
DOI: 10.1098/rsta.1896.0007

Accurate Experimental Electronic Properties of DL-Proline Monohydrate Obtained Within 1 Day
journal, January 1998

Koritsanszky, T.
Science, Vol. 279, Issue 5349
DOI: 10.1126/science.279.5349.356

Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature
journal, February 2013

Kern, J.; Alonso-Mori, R.; Tran, R.
Science, Vol. 340, Issue 6131
DOI: 10.1126/science.1234273

Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts
journal, January 2015

Subramanian, Ganesh; Basu, Shibom; Liu, Haiguang
Ultramicroscopy, Vol. 148
DOI: 10.1016/j.ultramic.2014.08.013

Structural Studies with X Rays
journal, June 1965

Kraut, J.
Annual Review of Biochemistry, Vol. 34, Issue 1
DOI: 10.1146/annurev.bi.34.070165.001335

Similarity measures between images
journal, January 1987

Van Heel, Marin
Ultramicroscopy, Vol. 21, Issue 1
DOI: 10.1016/0304-3991(87)90010-6

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
journal, January 1992

Brünger, Axel T.
Nature, Vol. 355, Issue 6359
DOI: 10.1038/355472a0

Estimation of the quality of refined protein crystal structures: The Quality of Protein Structures
journal, March 2015

Wang, Jimin
Protein Science, Vol. 24, Issue 5
DOI: 10.1002/pro.2639

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
journal, March 2015

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.
eLife, Vol. 4
DOI: 10.7554/eLife.05421

X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis
journal, August 1990

Wang, Jimin; Mauro, J. Matthew; Edwards, Steven L.
Biochemistry, Vol. 29, Issue 31
DOI: 10.1021/bi00483a003

Effects of aligned α-helix peptide dipoles on experimental electrostatic potentials: Long-Range ESP and Dipole Moment
journal, June 2017

Wang, Jimin; Videla, Pablo E.; Batista, Victor S.
Protein Science, Vol. 26, Issue 9
DOI: 10.1002/pro.3204

Similar Records in DOE PAGES and OSTI.GOV collections:

Weak data do not make a free lunch, only a cheap meal

Journal Article Luo, Zhipu ; Rajashankar, Kanagalaghatta ; Dauter, Zbigniew - Acta Crystallographica. Section D: Biological Crystallography (Online)

Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria of resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such asR_mergeandI/σ(I), optical resolution and the correlation coefficients CC_1/2and CC*, can be used for judging the internal data quality, whereas the reliability factorsRandR_freeas well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of thesemore »« less
https://doi.org/10.1107/S1399004713026680
Nickel deficiency in RENi{sub 2-x}P{sub 2} (RE=La, Ce, Pr). Combined crystallographic and physical property studies

Journal Article Bobev, Svilen ; Xia, Sheng-qing ; Bauer, Eric D ; ... - Journal of Solid State Chemistry

Large single crystals from RENi{sub 2-x}P{sub 2} (RE=La, Ce, Pr) were synthesized from the pure elements using Sn as a metal flux, and their structures were established by X-ray crystallography. The title compounds were confirmed to crystallize in the body-centered tetragonal ThCr{sub 2}Si{sub 2} structure type (space group I4/mmm (No. 139); Pearson's symbol tI10), but with a significant homogeneity range with respect to the transition metal. Systematic synthetic work, coupled with accurate structure refinements indicated strong correlation between the degree of Ni-deficiency and the reaction conditions. According to the temperature dependent dc magnetization measurements, LaNi{sub 2-x}P{sub 2} (x=0.30(1)), as expected,more »« less
https://doi.org/10.1016/j.jssc.2009.03.014
Nickel deficiency in RENi2-xP2 (RE=La, Ce, Pr). Combined crystallographic and physical property studies

Journal Article Bauer, Eric D ; Ronning, Filip ; Thompson, Joe D ; ... - Journal of Solid State Chemistry

Large single crystals from RENi{sub 2-x}P{sub 2} (RE = La, Ce, Pr) were synthesized from the pure elements using Sn as a metal flux, and their structures were established by X-ray crystallography. The title compounds were confirmed to crystallize in the body-centered tetragonal ThCr{sub 2}Si{sub 2} structure type (space group I4/mmm (No. 139); Pearson's symbol tI10), but with a significant stoichiometry breadth with respect to the transition metal. Systematic synthetic work, coupled with accurate structure refinements indicated strong correlation between the degree of Ni-deficiency and the reaction conditions. For four different PrNi{sub 2-x}P{sub 2} (x {le} 0.5) samples, temperature dependentmore »« less
Full Text Available
Gaussian basis sets for use in correlated molecular calculations. V. Core-valence basis sets for boron through neon

Journal Article Woon, D E ; Dunning, Jr, T H - Journal of Chemical Physics

The correlation-consistent polarized valence basis sets (cc-pVXZ) for the atoms boron through neon have been extended to treat core and core-valence correlation effects. Basis functions were added to the existing cc-pVXZ sets to form correlation-consistent polarized core-valence sets (cc-pCVXZ) in the usual pattern: Double zeta added (1{ital s}1{ital p}), triple zeta added (2{ital s}2{ital p}1{ital d}), quadruple zeta added (3{ital s}3{ital p}2{ital d}1{ital f}), and quintuple zeta added (4{ital s}4{ital p}3{ital d}2{ital f}1{ital g}). The exponents of the core functions were determined by minimizing the {ital difference} between all-electron and valence-only correlation energies obtained from HF+1+2 calculations on the groundmore »« less
https://doi.org/10.1063/1.470645
High accuracy barrier heights, enthalpies, and rate coefficients for chemical reactions

Journal Article Spiekermann, Kevin ; Pattanaik, Lagnajit ; Green, William H. - Scientific Data

Absmore »« less
https://doi.org/10.1038/s41597-022-01529-6

Similar Records

Title: On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets

Abstract

Citation Formats

Linking Crystallographic Model and Data Quality journal, May 2012

On the appearance of carboxylates in electrostatic potential maps: ESP Involving Carboxylate Groups journal, December 2016

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures journal, September 2014

Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy journal, October 2003

Structure of photosystem II and substrate binding at room temperature journal, November 2016

The significance of the phase synthesis journal, May 1961

An Apparent Paradox in Crystal Structure Analysis journal, April 1961

The probability distribution of X-ray intensities journal, October 1949

Serial crystallography on in vivo grown microcrystals using synchrotron radiation journal, February 2014

The mode of attachment of the azide ion to sperm whale metmyoglobin journal, January 1964

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals journal, June 2012

Largest likely values for the reliability index journal, September 1950

Assessing and maximizing data quality in macromolecular crystallography journal, October 2015

Identification of rogue datasets in serial crystallography journal, April 2016

Largest likely values of residuals journal, November 1974

Modeling truncated pixel values of faint reflections in MicroED images journal, May 2016

Accurate model annotation of a near-atomic resolution cryo-EM map journal, March 2017

Experimental charge density from electron microscopic maps: Laplacian Operation on ESP Maps journal, May 2017

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL journal, February 2017

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy journal, July 2014

On the interpretation of electron microscopic maps of biological macromolecules: Electric Potentials Involving Negative Charges journal, October 2016

New statistical tests for distinguishing between centrosymmetric and non-centrosymmetric structures journal, November 1966

Why phase errors affect the electron function more than amplitude errors journal, February 2008

Serial crystallography using synchrotron radiation journal, February 2014

Mathematical Contributions to the Theory of Evolution. III. Regression, Heredity, and Panmixia journal, January 1896

Accurate Experimental Electronic Properties of DL-Proline Monohydrate Obtained Within 1 Day journal, January 1998

Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature journal, February 2013

Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts journal, January 2015

Structural Studies with X Rays journal, June 1965

Similarity measures between images journal, January 1987

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures journal, January 1992

Estimation of the quality of refined protein crystal structures: The Quality of Protein Structures journal, March 2015

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals journal, March 2015

X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis journal, August 1990

Effects of aligned α-helix peptide dipoles on experimental electrostatic potentials: Long-Range ESP and Dipole Moment journal, June 2017

Linking Crystallographic Model and Data Quality
journal, May 2012

On the appearance of carboxylates in electrostatic potential maps: ESP Involving Carboxylate Groups
journal, December 2016

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures
journal, September 2014

Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy
journal, October 2003

Structure of photosystem II and substrate binding at room temperature
journal, November 2016

The significance of the phase synthesis
journal, May 1961

An Apparent Paradox in Crystal Structure Analysis
journal, April 1961

The probability distribution of X-ray intensities
journal, October 1949

Serial crystallography on in vivo grown microcrystals using synchrotron radiation
journal, February 2014

The mode of attachment of the azide ion to sperm whale metmyoglobin
journal, January 1964

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals
journal, June 2012

Largest likely values for the reliability index
journal, September 1950

Assessing and maximizing data quality in macromolecular crystallography
journal, October 2015

Identification of rogue datasets in serial crystallography
journal, April 2016

Largest likely values of residuals
journal, November 1974

Modeling truncated pixel values of faint reflections in MicroED images
journal, May 2016

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

Experimental charge density from electron microscopic maps: Laplacian Operation on ESP Maps
journal, May 2017

Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL
journal, February 2017

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy
journal, July 2014

On the interpretation of electron microscopic maps of biological macromolecules: Electric Potentials Involving Negative Charges
journal, October 2016

New statistical tests for distinguishing between centrosymmetric and non-centrosymmetric structures
journal, November 1966

Why phase errors affect the electron function more than amplitude errors
journal, February 2008

Serial crystallography using synchrotron radiation
journal, February 2014

Mathematical Contributions to the Theory of Evolution. III. Regression, Heredity, and Panmixia
journal, January 1896

Accurate Experimental Electronic Properties of DL-Proline Monohydrate Obtained Within 1 Day
journal, January 1998

Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature
journal, February 2013

Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts
journal, January 2015

Structural Studies with X Rays
journal, June 1965

Similarity measures between images
journal, January 1987

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
journal, January 1992

Estimation of the quality of refined protein crystal structures: The Quality of Protein Structures
journal, March 2015

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
journal, March 2015

X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis
journal, August 1990

Effects of aligned α-helix peptide dipoles on experimental electrostatic potentials: Long-Range ESP and Dipole Moment
journal, June 2017