TABLE 1.
Crystallographic and refinement data of StCBM64C from Spirochaeta thermophile
Statistics for the highest resolution shell are shown in parentheses. 2NV, Jeffamine ED-2001; SSN, 4-oxobutanoic acid; FMT, formic acid.
| StCBM64C | StCBM64C sulfur-SAD | |
|---|---|---|
| Crystallographic data | ||
| Source | PXII (X06DA), SLS | PXII (X06DA), SLS |
| Detector | PILATUS 2M-F | PILATUS 2M-F |
| Wavelength (Å) | 1.0 | 1.8 |
| a (Å) = b (Å) | 56.70 | 56.72 |
| c (Å) | 66.74 | 66.74 |
| Space group | P43212 | P43212 |
| Molecules per ASU | 1 | 1 |
| Matthews coefficient (Å3·Dalton−1) | 2.71 | 2.71 |
| Mosaicity (°) | 0.18 | 0.11 |
| Resolution range (Å) | 43.21–1.53 (1.53–1.50) | 43.19–2.38 (2.38–2.30) |
| <I/σI> | 79.4 (16.0) | 129.0 (92.3) |
| Wilson B-factor | 13.3 | 14.3 |
| Rmerge (%)a | 2.8 (9.2) | 3.4 (4.4) |
| Rpim (%)b | 0.6 (4.0) | 0.5 (0.7) |
| Half-data set correlation CC½ | 1.00 (0.94) | 1.00 (1.00) |
| Multiplicity | 21.8 (6.8) | 45.6 (41.7) |
| No. of observed reflections | 394529 (5954) | 237504 (20201) |
| No. of unique reflections | 18085 (870) | 5212 (484) |
| Completeness (%) | 99.9 (99.0) | 99.9 (98.7) |
| Anomalous completeness (%) | 99.4 (89.4) | 99.8 (98.3) |
| Anomalous multiplicity | 11.6 (3.4) | 25.4 (22.3) |
| Figure of merit for two sulfur sites (before/after solvent flattening) | 0.40/0.91 | |
| Refinement statistics | ||
| Rworkc | 0.1237 | |
| Rfreed | 0.1511 | |
| Root mean square deviation bonds (Å) | 0.013 | |
| Root mean square deviation angles (°) | 1.349 | |
| Average B (Å2) | 17.20 | |
| Main chain | 13.3 | |
| Side chain | 16.1 | |
| Water molecules | 32.5 | |
| Ca2+ A/B | 36.1 (occe 0.35)/21.0 (occe 0.43) | |
| Ni2+ | 20.7 (occe 0.24) | |
| 2NV | 30.6 (occe 1.0) | |
| SSN | 41.3 (occe 1.0) | |
| FMT | 19.4 (occe 1.0) | |
| Amino acid residues per ASU | 88 | |
| Ligands per ASU | 2NV, Ca2+, Ni2+, SSN, FMT | |
| No. of water molecules | 87 | |
| Total no. of atoms | 888 | |
| Ramachandran favored (%) | 98.9 | |
| Ramachandran outliers (%) | 0.0 | |
a Rmerge = [Σ|I − <I>|]/Σ<I>, where I is the observed intensity, and <I> is the statistically weighted average intensity of multiple observations.
b Rpim = [Σ √(1/(n − 1)) Σ|I − <I>|]/Σ <I>, a redundancy-independent version of Rmerge.
c Rwork = Σ||Fcalc| − |Fobs||/Σ|Fobs| × 100, where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively.
d Rfree is calculated for a randomly chosen 5% of the reflections.
e occ, occupancy.