Table 1.
Data collection, refinements, statistics, and validation. Highest-resolution shell is shown in parentheses.
| Data Collection | OleP–DEOLS | OleP–DEOHS | OleP–DEO-Rhamnose | OleP–6DEB–Rhamnose |
|---|---|---|---|---|
| PDB ID | 6ZI2 | 6ZHZ | 6ZI7 | 6ZI3 |
| Crystallization Conditions | 0.2 M NaCl 0.1 M Tris·HCl pH 7.4 25% PEG 3350 (seeding) |
4 M HCOONa (10% glycerol) |
4.4 M HCOONa | 4.2 M HCOONa (20% glycerol) |
| Space group | P1 | C2 | C2 | C2 |
| Unit cell (Å, °) | a = 112.07, b = 116.64, c = 125.17, α = 104.43, β = 104.25, γ = 113.91 |
a = 247.47, b = 111.22, c = 159.20, β = 129.4 |
a = 247.53, b = 110.68, c = 159.28, β = 129.5 |
a = 247.38, b = 111.15, c = 159.14, β = 129.4 |
| Resolution (å) | 39.89–2.87 (3.05–2.87) |
37.7–2.20 (2.33–2.20) |
50.0–2.11 (2.24–2.11) |
50.0–1.96 (2.08–1.96) |
| Total measurements | 411,472 | 574,285 | 1,262,482 | 1,251,578 |
| Unique reflections | 115,590 | 168,218 | 373,419 | 462,663 |
| Completeness (%) | 98.2 (95.9) | 98.9 (97.3) | 99.1 (99.0) | 97.7 (96.7) |
| Redundancy | 3.56 (3.64) | 3.41 (3.37) | 3.38 (3.30) | 2.70 (2.54) |
| Rmerge a (%) | 16.5 (92.4) | 5.6 (112.7) | 7.2 (147.1) | 6.4 (163.6) |
| cc/2 (%) | 99.0 (68.8) | 99.8 (51.4) | 99.8 (48.4) | 99.7 (36.2) |
| I/σ (I) | 7.29 (1.36) | 12.10 (1.05) | 10.52 (0.72) | 7.80 (0.52) |
| Wilson B-value (Å2) | 44.1 | 44.9 | 56.7 | 53.5 |
| Refinement | ||||
| Molecules per asymmetric unit |
9 | 6 | 6 | 6 |
| Resolution Range (Å) | 39.89–2.93 | 37.73–2.2 | 47.92–2.28 | 48.09–2.08 |
| Rwork/Rfree b (%) | 24.0/29.1 | 18.7/24.3 | 18.4/24.7 | 17.2/22.5 |
| Deviations from ideal geometry | ||||
| Bond (Å) | 0.011 | 0.012 | 0.013 | 0.011 |
| Angles (°) | 1.78 | 2.16 | 2.16 | 1.75 |
| Ramachandran (%) Favored/allowed/outliers * |
96.6/3.4/0.0 | 96.1/3.9/0.0 | 96.6/3.4/0.0 | 97.0/3.0/0.0 |
| Mean B-factors (Å2) | ||||
| Protein | 56.9 | 45.2 | 59.5 | 59.6 |
| HEM/DEO/6DEB/RAM | 51.3/53.5/-/- | 31.7/44.7/-/- | 43.1/46.8/-/54.6 | 42.8/-/47.2/75.7 |
| H2O/Na/FMT/GOL/TRS | 13.5/-/-/-/- | 62.2/58.5/87.5/81.6/64.4 | 59.6/56.1/76.4/- | 63.9/86.7/55.9/83.3/87.6 |
| RSCC (per monomer in the asymmetric unit) | ||||
| DEO | 0.88/0.96/0.95/0.91/0.88/0.88/0.88/0.88/0.80 | 0.97/0.96/0.97/0.95/0.95/0.95 | 0.97/0.97/0.97/0.97/0.96/0.96 | |
| 6DEB | 0.98/0.93/0.96/0.93/0.97/0.97 | |||
| RAM (bound to the solvent cavity) | 0.91;0.86/0.81/-/0.85/-/- | 0.87/0.80/0.86/0.87/0.85/- | ||
| No of Atoms | ||||
| Protein | 26350 | 18824 | 19903 | 20575 |
| HEM/DEO/6DEB/RAM | 387/234/-/- | 258/156/-/- | 258/156/-/33 | 258/-/162/77+ |
| H2O/Na+/FMT/GOL/TRS | 96/-/-/-/- | 763/5/249/90/24 | 1369/6/642/-/- | 1145/7/609/36/24 |
a, where i runs over multiple observations of the same intensity, and j runs over all crystallographically unique intensities. b , where |Fobs| > 0. Rfree is based on 5% of the data randomly selected and is not used in the refinement. * No prolines and glycines. + In OleP–6DEB–rhamnose, two out of seven total L-rhamnose molecules (RAM) found are bound to the external surface.