Table 1.
Refinement statistics
| pdb code | 3O1F | 2W9R | 3O2H | 2WA8 | 3O2B | 2WA9 | 3O2O |
|---|---|---|---|---|---|---|---|
| E. coli ClpS residues | 26-106 | 2-108 ((b)) | 2-106 | 2-106 | 2-108 ((b)) | 2-106 ((c)) | |
| N-end peptide | none | LVKSKATNLLY | FRSKGEELFT | unclear ((d)) | none | ||
| space group | P1 | P1 | P1211 | C2 | |||
| unit cell a = | 28.0 Å | 28.1 Å | 32.2 Å | 171.9 Å | |||
| unit cell b = | 28.1 Å | 28.2 Å | 58.4 Å | 155.9 Å | |||
| unit cell c = | 51.6 Å | 38.9 Å | 56.4 Å | 71.2 Å | |||
| unit cell α = | 80.5° | 97.4° | 90.0° | 90.0° | |||
| unit cell β = | 77.9° | 106.5° | 101.9° | 114.6° | |||
| unit cell γ = | 72.3° | 92.4° | 90.0° | 90.0° | |||
| subunits/peptides per asu | 2/0 | 1/1 | 2/2 | 7/7 | 8/0 | ||
| refinement resolution | 22.5 - 1.4 Å | 25.0 - 1.7 Å | 30.2 - 2.15 Å | 30.2 - 2.05 Å | 25.0 - 2.9 Å | ||
| wavelength | 1.54 Å | 0.978 Å | 1.071 Å | 1.071 Å | |||
| Rsym (%) | 3.6 | 3.9 (20.9) | 11.3 (45.1) | 13.7 (73.6) | |||
| unique reflections | 23635 | 11540 | 9909 | 12292 | 19203 | ||
| completeness (%) | 82.4 (32) | 91.1 (86.1) | 94.0 (90.5) | 94.9 (96.0) | 99.3 (96.3) | ||
| data redundancy | 3.7 (3.1) | 2.2 (2.0) | 2.9 (2.7) | 7.5 (7.3) | |||
| average I/σI | 25.1 (5.2) | 12.4 (3.9) | 6.5 (2.3) | 11 (2.0) | |||
| Rwork (%) | 17.3 (21.7) | 22.6 (27.8) | 19.7 (25.6) | 22.5 (26.0) | 21.1 (27.1) | 23.7 (26.1) | 17.3 (29.4) |
| Rfree (%) | 19.7 (21.0) | 25.4 (32.8) | 22.7 (33.2) | 26.8 (33.5) | 24.8 (31.8) | 24.8 (28.5) | 20.1 (32.1) |
| TLS | no | yes ((e)) | no | no | no | yes | no |
| r.m.s.d. bond lengths (Å) | 0.007 | 0.009 | 0.009 | 0.010 | 0.006 | 0.015 | 0.005 |
| r.m.s.d. bond angles (°) | 1.19 | 1.19 | 1.17 | 1.54 | 1.02 | 1.57 | 0.79 |
| total protein atoms including H | 2637 | 861 (no H) | 1712 | 1660 (no H) | 3199 | 4880 (no H) | 10767 |
| solvent atoms | 402 | 68 | 128 | 91 | 140 | 0 | 0 |
| average B value | 17.9 | 22.1 | 24.1 | 33.2 | 33.6 | 50.0 | 73.7 |
| Ramachandran ((a)) favored/allowed/disallowed (%) |
100/0/0 | 100/0/0 | 100/0/0 | 93.5/3.0/3.5 | 100/0/0 | 94.4/2.0/3.6 | 99.5/0.5/0 |
| favorable rotamers (%) ((a)) | 100 | 93.6 | 100 | 89.9 | 100 | 89.7 | 100 |
| clash score ((a)) | 0.0 | 5.8 | 0.0 | 18.7 | 0 | 17.1 | 0 |
| Cβ deviations > 0.25 Å ((a)) | 0 | 0 | 0 | 3 | 0 | 4 | 0 |
| residues with bad angles ((a)) | 0 | 0 | 0 | 1 | 0 | 0 | |
| cis peptide bonds | 0 | 0 | 0 | 8 | 0 | 0 | 0 |
Numbers in parenthesis represent values for the highest resolution bin. Unit cell and data collection statistics for the rerefined structures are from Schuenemann et al. (2009).
Favorable/allowed/disallowed Ramachandran angles, favorable rotamers, Cβ deviations, residues with bad angles, and the clash score (number of steric overlaps ≥ 0.4 Å per 1000 atoms) were calculated using MolProbity (Davis et al., 2007).
The original 2W9R and 2WA9 structures (Schuenemann et al., 2009) contain two additional C-terminal residues that are not present in the protein sequence. In our re-refined structures, there was no density for these “extra” residues and the chain terminated with Ala106 as expected.
As discussed in the text, it is possible that the polypeptide was cleaved between Ala21 and Leu22.
The peptide sequence is listed as LLT in the pdb file but as WRSKGEELFTGV in Schuenemann et al. (2009). In our rerefined structure, there was no peptide. Instead, an N-terminal segment of a neighboring ClpS molecule occupied the binding pocket.
ANISOU records are included in the 2W9R pdb file, although the header reports no TLS groups.
Rsym = ShSj ∣Ij(h) - <I(h)>∣ / ShSj <I(h)>, where Ij(h) is the jth reflection of index h and <I(h)> is the average intensity of all observations of I(h).
Rwork = Sh ∣Fobs(h) – Fcalc(h)∣ ∣ / Sh ∣Fobs(h)∣, calculated over the 93-95% of the data in the working set. Rfree equivalent to Rwork except calculated over 5-7% of the data assigned to the test set.