Table I.
Data Collection and Refinement Statistics
| Crystal | C. hiranonis DSM 13275 | C. scindens ATCC 35704 | C. hylemonae DSM 15053 | C. hiranonis DSM 13275:3-oxo- Δ4,6-LC-CoA | ||
|---|---|---|---|---|---|---|
| PDB id | 4L8P | 4LEH | 4L8O | 4N3V | ||
| Space group | P63 | P3121 | R32:h | R32:h | ||
| Unit cell lengths (Å) | a=b=58.9,c=91.3 | a=b=109.3,c=118.3 | a=b=53.0,c=428.6 | a=b=84.3,c=311.8 | ||
| Data collection | ||||||
| Beamline | SSRL BL11-1 | SSRL BL11-1 | ALS 8.2.2 | ALS 8.2.2 | ||
| Data set | SAD | λ1 MAD | λ2 MAD | λ3 MAD | Native | Native |
| Wavelength (Å) | 0.9795 | 0.9790 | 0.9795 | 0.9184 | 1.000 | 1.000 |
| Resolution range (Å) | 29.45–1.60 | 29.57–2.90 | 29.55–2.98 | 29.54–2.90 | 28.58–2.20 | 47.40–1.89 |
| Highest resolution shell (Å) | 1.64–1.60 | 2.98–2.90 | 3.06–2.98 | 2.98–2.90 | 2.32–2.20 | 1.94–1.89 |
| No. of observations | 172,513 | 137,535 | 63,001 | 68,430 | 77,498 | 362,382 |
| No. of unique reflections | 23,715 | 18,559 | 17,071 | 18,502 | 12,340 | 34,714 |
| Completeness (%) | 100 (100)a | 99.9 (100) | 99.9 (100) | 99.9 (100) | 99.3 (96.0) | 99.9 (98.8) |
| Mean I/σ(I) | 11.1 (2.7)a | 13.1 (1.8) | 11.3 (2.0) | 11.2 (1.8) | 17.1 (2.7) | 19.5 (2.5) |
| Rmerge on Ib (%) | 9.5 (65.1)a | 9.4 (112.3) | 7.3 (61.8) | 7.1 (73.0) | 9.5 (55.7) | 6.9 (88.5) |
| Rmeas on Ic (%) | 10.2 (70.3)a | 10.1 (120.6) | 8.5 (72.3) | 8.3 (85.5) | 10.4 (61.9) | 7.3 (95.3) |
| Rpim on Id (%) | 3.8 (26.4)a | 3.7 (43.5) | 4.4 (36.8) | 4.2 (43.8) | 4.1 (26.4) | 2.2 (35.0) |
| Model and refinement statistics | ||||||
| Data used in refinement | λ1 MAD | |||||
| No. of reflections (total)g | 23,680 | 18,530 | 11,786 | 34,711 | ||
| No. of reflections (test) | 1,222 | 948 | 568 | 1,748 | ||
| Cutoff criteria | |F|>0 | |F|>0 | |F|>0 | |F|>0 | ||
| Rcryst (%)e | 15.1 | 17.7 | 19.4 | 18.8 | ||
| Rfree (%)f | 18.1 | 21.7 | 22.5 | 21.8 | ||
| Stereochemical parameters | ||||||
| Restraints (RMSD observed) | ||||||
| Bond lengths (Å) | 0.011 | 0.011 | 0.013 | 0.010 | ||
| Bond angles (°) | 1.49 | 1.49 | 1.32 | 1.38 | ||
| MolProbity statistics | ||||||
| Ramachandran plot (%)h | 97.6 (0) | 98.0 (0) | 98.8 (0) | 99.4 (0) | ||
| Rotamer outliers (%) | 2.1 | 0.7 | 0.0 | 2.1 | ||
| All atom clashscore | 1.4 | 1.0 | 0.4 | 3.2 | ||
| Average isotropic B-value (Å2)i | 24.8 (17.7) | 96.3 (104.1) | 35.2 (39.4) | 35.8 (26.2) | ||
| ESU based on Rfree (Å) | 0.08 | 0.31 | 0.18 | 0.13 | ||
| Protein residues/atoms | 168/1366 | 501/4091 | 168/1335 | 334/2722 | ||
| Non-protein entities | 124 H2O, 1 Ni+, 1 Na+, 2 PEG fragments |
3 H2O, 8 SO42−, 1 Zn2+ | 70 H2O, 1 SO42−, 1 Co2+, 1 Na+, 4 ethylene glycol | 189 H2O, 1 UNL, 2 Zn2+, 2 Na+, 2 citric acid, 1 ethylene glycol, 1 PEG fragment | ||
Values in the parentheses are for the highest resolution shell.
Rmerge=ΣhklΣi|Ii(hkl)−<I(hkl)>|/ΣhklΣiIi(hkl)
Rmeas(redundancy-independent Rmerge) =Σhkl[Nhkl/(Nhkl−1)]1/2Σi|Ii(hkl)−<I(hkl)>|/ΣhklΣiIi(hkl)
Rpim(precision-indicating Rmerge)=Σhkl[1/(Nhkl−1)]1/2Σi|Ii(hkl)−<I(hkl)>|/ΣhklΣiIi(hkl)
Rcryst =Σ| |Fobs|−|Fcalc| |/Σ|Fobs|, where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively.
Rfree = as for Rcryst, but for 5% of the total reflections chosen at random and omitted from refinement.
Typically, the number of unique reflections used in refinement is slightly less than the total number that were integrated and scaled. Reflections are excluded due to systematic absences, negative intensities and rounding errors in the resolution limits and cell parameters.
Percentage of residues in favored regions (Top8000) of Ramachandran plot (outliers in parenthesis).
This value represents the total B that includes TLS and residual B components. (Wilson plot B-value in parenthesis.)