Table 1.
Data-collection and refinement statistics of EcCdnD crystals. See below for some description about the listed items
| Native | ddATP | ATP+ADP | AMPcPP | KK-ATP | |
|---|---|---|---|---|---|
| Data collection | |||||
| Space group | P41212 | P41212 | P21 | C2221 | C2221 |
| Unit-cell a, b, c (Å) | 52.9, 52.9, 344.4 | 53.2, 53.2, 345.8 | 65.8, 107.2, 65.9 | 66.3, 116.4, 107.4 | 68.9, 118.2, 102.4 |
| Unit-cell α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 118.3, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution range (Å) | 30–2.14 (2.22–2.14) | 50–2.09 (2.16–2.09) | 30–1.87 (1.94–1.87) | 50–1.93 (2.00–1.93) | 30–2.70 (2.80–2.70) |
| Unique reflections | 27 647 (2654) | 30 653 (2873) | 66 128 (6346) | 31 398 (3124) | 11 739 (1142) |
| Redundancy | 8.7 (6.5) | 9.7 (5.0) | 3.8 (3.7) | 7.0 (7.1) | 6.9 (6.6) |
| Completeness (%) | 98.9 (97.5) | 99.1 (96.7) | 99.5 (95.2) | 99.9 (100.0) | 99.7 (99.2) |
| Average I/σ(I) | 17.0 (2.7) | 25.0 (3.4) | 29.0 (8.5) | 25.7 (3.6) | 17.1 (2.9) |
| Average CC1/2 | 0.988 (0.969) | 0.985 (0.943) | 0.992 (0.974) | 0.986 (0.950) | 0.961 (0.838) |
| Rmerge (%) | 9.6 (40.3) | 8.3 (37.2) | 4.3 (15.4) | 7.2 (51.4) | 11.3 (63.3) |
| Rpim (%) | 3.6 (16.1) | 2.7 (16.0) | 2.6 (9.3) | 3.0 (20.5) | 4.6 (26.0) |
| Structure refinement | |||||
| Resolution range (Å) | 24–2.15 (2.23–2.15) | 28–2.09 (2.17–2.09) | 29–1.87 (1.94–1.87) | 34–1.93 (2.00–1.93) | 24–2.70 (2.80–2.70) |
| No. of reflections | 24 213 (1206) | 28 906 (1722) | 66 096 (6464) | 31 018 (2713) | 11 641 (1042) |
| Completeness (%) | 86.7 (44.5) | 93.9 (58.3) | 99.7 (97.3) | 98.4 (87.0) | 98.8 (90.7) |
| Rwork for 95% data (%) | 18.2 (21.5) | 17.6 (20.9) | 13.6 (15.7) | 15.2 (19.7) | 19.2 (24.1) |
| Rfree for 5% data (%) | 22.8 (30.4) | 21.0 (24.2) | 16.3 (19.6) | 19.2 (22.2) | 25.0 (33.0) |
| RMSD bond lengths (Å) | 0.0029 | 0.0037 | 0.0120 | 0.0079 | 0.0019 |
| RMSD bond angles (°) | 0.593 | 0.749 | 1.216 | 0.897 | 0.648 |
| Bave (Å2)/protein atoms | 37.7/2877 | 29.4/2793 | 20.4/5619 | 22.0/2803 | 42.9/2773 |
| Bave (Å2)/ligand atoms | 30.9/1 | 41.6/31 | 22.5/170 | 19.4/66 | 35.6/62 |
| Bave (Å2)/water molecules | 46.1/371 | 40.8/373 | 33.7/935 | 36.6/454 | 43.4/206 |
| Ramachandran favored (%) | 98.0 | 99.1 | 98.1 | 98.2 | 97.9 |
| Ramachandran allowed (%) | 2.0 | 0.9 | 1.9 | 1.8 | 2.1 |
| Ramachandran outliers (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| Clashscore | 2.64 | 2.52 | 3.41 | 1.94 | 4.65 |
| MolProbity score | 1.13 | 1.04 | 1.13 | 0.96 | 1.53 |
| PDB code | 7D48 | 7D4J | 7D4O | 7D4S | 7D4U |
Numbers in parentheses are for the highest resolution shells.
I/σ(I) = ratio of intensity against background, or signal-noise level
CC1/2 = correlation coefficient between intensity estimates of half data sets
R merge = merging R factor = Σh Σi|<Ih> – Ih,i|/Σh ΣiIh,I where h and i enumerate unique reflections and symmetry-equivalent contributors.
R pim = precision-indicating merging R factor = Σh [1/(nh – 1)]1/2 Σi|<Ih> – Ih,i|/Σh ΣiIh,i where nh denotes multiplicity.
R work = R value for the working data subset used in the refinement = Σh | Fh,obs – Fh,calc |/ ΣhFh,obs where Fh,obs and Fh,calc are the observed and calculated structure factors.
R free = R value for the free data subset not used in the refinement to monitor the correctness of the model and the progress of refinement.
The RMSDs are root-mean-square deviations of the bond lengths and bond angles in the refined models from the ideal values in the dictionary of MolProbity (27)
B ave = average isotropic temperature factors over the numbers of specified atoms.
The numbers of amino acid residues in the favored and allowed regions of Ramachandran plot for the peptide dihedral angles were determined by MolProbity, as well as the clash scores, which represent the numbers of serious clashes per 1000 atoms.
The MolProbity score serves as a single composite metric for model quality (lower numbers indicate better models).