addenda and errata\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047

Novel c-di-GMP recognition modes of the mouse innate immune adaptor protein STING. Corrigendum

aAgricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, bInstitute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, cGraduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan, dInstitute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, eDepartment of Cell Biology, University of Miami School of Medicine, Miami, Florida, USA, and fSchool of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
*Correspondence e-mail: shchou@nchu.edu.tw

(Received 2 May 2013; accepted 2 May 2013; online 17 May 2013)

The two structures reported in the article by Chin et al. [(2013). Acta Cryst. D69, 352–366] have been further refined and corrected.

The original structures reported in the article by Chin et al. (2013[Chin, K.-H., Tu, Z.-L., Su, Y.-C., Yu, Y.-J., Chen, H.-C., Lo, Y.-C., Chen, C.-P., Barber, G. N., Chuah, M. L.-C., Liang, Z.-X. & Chou, S.-H. (2013). Acta Cryst. D69, 352-366.]) were incorrectly modeled in the C-terminal region, and contained some notable geometrical deviations. The structures have now been corrected, refined again and validated with MolProbity (Chen et al., 2010[Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.]). The improved structures have been re-deposited in the PDB with the same PDB codes (mSTING-CTD, 4g3l and mSTING-CTD–c-­di-GMP complex, 4g4d ). A corrected Table 1[link] is given below. The conclusions of the paper are not changed by these corrections.

Table 1
Summary of the crystallographic data for mSTING and the mSTING–c-di-GMP complex

Values in parentheses are for the outermost shell.

  Native SeMet-mSTING mSTING–c-di-GMP
Beamline BL13C1 BL13B1 SP44XU
Wavelength (Å) 0.97622 0.97898 0.99808
Space group P31 P31 P31
Unit-cell parameters (Å, °) a = b = 78.619, c = 50.418, α = β = 90, γ = 120 a = b = 78.493, c = 50.409, α = β = 90, γ = 120 a = b = 79.058, c = 49.693, α = β = 90, γ = 120
Resolution range (Å) 30–2.39 (2.48–2.39) 30–2.20 (2.28–2.20) 30–2.36 (2.44–2.36)
Total observations 44542 (4387) 125788 (12546) 41778 (5210)
Unique observations 13794 (1371) 17676 (1767) 14245 (1444)
Multiplicity 3.2 (3.2) 7.1 (7.1) 2.9 (2.9)
Completeness (%) 100 (100) 100 (100) 99.6 (100)
Rmerge (%) 6.1 (59.5) 6.5 (44.7) 3.9 (41.0)
I/σ(I)〉 19.4 (2.3) 23.8 (4.9) 17.4 (2.8)
Rfree test-set size (%) 5 5 5
Refinement statistics
Rcryst/Rfree§ (%) 22.5/25.1 19.3/25.1 19.7/26.3
Model content
 Protein residues 370 368 352
 c-di-GMP molecules 0 0 1
 Mg2+ ions 2 2 0
 Waters 205 158 124
Average B factors (Å2)
 Backbone atoms 41.8 43.7 41.8
 Side-chain atoms 43.6 45.2 44.6
 Water O atoms 52.9 51.3 53.1
 c-di-GMP molecules     58.9
Ramachandran plot, residues in (%)
 Most favourable regions 93.1 97.1 93.3
 Additionally allowed regions 0.9 2.9 6.1
 Outliers 0 0.6
Rotamer outliers (%) 2.8 0.9
R.m.s.d. from ideal geometry
 Bonds (Å) 0.008 0.0077 0.008
 Angles (°) 1.50 1.14 1.20
Rmerge = [\textstyle \sum_{hkl}\sum_{i}|I_{i}(hkl)- \langle I(hkl)\rangle|/][\textstyle \sum_{hkl}\sum_{i}I_{i}(hkl)].
Rcryst = [\textstyle \sum_{hkl}\big ||F_{\rm obs}|-|F_{\rm calc}|\big |/][\textstyle \sum_{hkl}|F_{\rm obs}|], where Fcalc and Fobs are the calculated and observed structure-factor amplitudes, respectively.
§Rfree is the same as Rcryst but for 5.0% of the total reflections chosen at random and omitted from refinement.
¶The percentages of residues located in the most favourable, additionally allowed regions and outliers were calculated using the MolProbity program with the default parameters (Chen et al., 2010[Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.]).

Supporting information


References

First citationChen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12–21.  Web of Science CrossRef CAS IUCr Journals
First citationChin, K.-H., Tu, Z.-L., Su, Y.-C., Yu, Y.-J., Chen, H.-C., Lo, Y.-C., Chen, C.-P., Barber, G. N., Chuah, M. L.-C., Liang, Z.-X. & Chou, S.-H. (2013). Acta Cryst. D69, 352–366.  Web of Science CrossRef CAS IUCr Journals

© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.

Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047
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