There are multiple errors in Table 1. Please see the corrected Table 1 here.
Table 1. Crystallographic data processing and refinement statistics.
| TcdA-ATP | TcdA-AMP | |
|---|---|---|
| PDB code | 4D79 | 4D7A |
| Data collection | ||
| Wavelength (Å) | 0.9795 | 0.9801 |
| Resolution range (Å) | 41.13–1.77 (1.83–1.77) | 41.14–1.80 (1.86–1.80) |
| Space group | P 1 21 1 | P 1 21 1 |
| Unit cell dimensions | ||
| a, b, c (Å) | 65.3, 96.7, 82.8 | 65.7, 97.2, 83.2 |
| β (°), α = γ = 90° | 90, 111.2, 90 | 90, 111.6, 90 |
| Total reflections | 312,887 (11,351) | 351,361 (33,129) |
| Unique reflections | 89,883 (5907) | 87,219 (8261) |
| Multiplicity | 3.5 (1.9) | 4.0 (4.0) |
| Completeness (%) | 95.96 (63.90) | 97.14 (92.68) |
| Mean I/σ(I) | 18.97 (3.75) | 19.93 (4.05) |
| Wilson B-factor | 23.95 | 21.59 |
| R-merge | 0.08388 (0.663) | 0.04687 (0.412) |
| R-meas a | 0.09797 | 0.05407 |
| CC1/2 b | 0.995 (0.556) | 0.999 (0.0.875) |
| CC* c | 0.999 (0.846) | 1.000 (0.966) |
| Refinement | ||
| R-work | 0.1416 (0.2994) | 0.1396 (0.1839) |
| R-free | 0.1833 (0.3236) | 0.1768 (0.2350) |
| # non-H atoms | 8167 | 8064 |
| # Protein atoms | 7484 | 7411 |
| # Ligand atoms | 172 | 46 |
| # Water | 511 | 607 |
| Protein residues | 996 | 974 |
| RMS(bonds) (Å) | 0.011 | 0.007 |
| RMS(angles) (°) | 1.430 | 1.01 |
| Ramachandran analysis | ||
| Favored/Allowed/Outlier (%) | 98.0/2.0/0.0 | 98.0/2.0/0.0 |
| Clashscore | 1.88 | 1.93 |
| Average B-factor (Å2) | 34.40 | 32.10 |
| Protein | 33.60 | 31.50 |
| Ligands | 60.80 | 49.70 |
| Solvent | 38.00 | 37.20 |
aRmeas = Σhkl (n/n-1)1/2 Σi |Ii(hkl)-<I(hkl)>| / ΣΣi Ii(hkl); where i is the ith measurement of reflection (hkl) and <I(hkl)> is the average over symmetry related observations of a unique reflection (hkl).
bCC1/2 is the Pearson correlation coefficient calculated between two random half data sets.
cCC* is the CC of the full data set against the true intensities, estimated from CC* = [2 CC1/2/(1+CC1/2)]1/2.
There is an error in the last sentence of the “TcdA crystallization, structure determination and refinement” subsection of the Materials and Methods. The correct sentence is: A data set for the AMP complex was collected to 1.80-Å resolution at the PROXIMA 2A beamline (Synchrotron SOLEIL, Paris, France). All the data sets were integrated with XDS [26] and scaled with Aimless [27] from the CCP4 suite of programs [28] (Table 1).
There are errors in the fifth and sixth sentences of the “Crystal structure of TcdA” subsection of the Results and Discussion. The correct sentences are: To shed light onto the structural basis for the tRNA binding and ct6A synthetic properties of TcdA-ATP, we determined the crystal structure of E. coli TcdA (Table 1 and Fig 2) loaded with ATP to 1.77 Å resolution (R/Rfree values of 0.141/0.183) (Fig 3A) and AMP to 1.80 Å resolution (R/Rfreevalues of 0.139/0.176) (Fig 3B). The asymmetric unit contained four TcdA chains arranged in two independent dimers, with a solvent content of 39%.
Reference
- 1. López-Estepa M, Ardá A, Savko M, Round A, Shepard WE, Bruix M, et al. (2015) The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily. PLoS ONE 10(4): e0118606 doi: 10.1371/journal.pone.0118606 [DOI] [PMC free article] [PubMed] [Google Scholar]