Table 2. Data-collection and refinement statistics.
Values in parentheses correspond to the high resolution range.
| CCA-adding enzyme | CCA-adding enzyme + CMPcPP | Nanobody 02 | Protease 1 | Lipase | RNA duplex | |
|---|---|---|---|---|---|---|
| X-ray beamline | PXIII, SLS | PXII, SLS | PX2A, SOLEIL | PXIII, SLS | ID30B, ESRF | PXIII, SLS |
| Wavelength (Å) | 1.000 | 1.000 | 0.826 | 1.240 | 0.976 | 0.826 |
| Temperature (K) | 293 | 293 | 293 | 293 | 293 | 293 |
| Detector | PILATUS 2M-F | PILATUS 6M | EIGER | PILATUS 2M-F | PILATUS3 6M | MAR CCD |
| Crystal-to-detector distance (mm) | 300 | 400 | 154 | 150/200 | 502 | 200 |
| Crystals collected | 6 | 14 | 9 | 1/11 | 14 | 3 |
| Crystals selected | 5 | 5 | 1 | 8 | 2 | 3 |
| Rotation range per image (°) | 0.1 | 0.2 | 0.1 | 0.2 | 0.1 | 2–3 |
| No. of images selected | 1000 | 540 | 500 | 1300 | 600 | 80 |
| Total rotation range (°) | 100 | 108 | 50 | 260 | 60 | 155 |
| Exposure time per image (s) | 0.1 | 0.1 | 0.1 | 0.1 | 0.02 | 1–2 |
| Space group | P43212 | P43212 | P43212 | P41212 | P61 | R3 |
| a, c (Å) | 71.5, 293.8 | 71.4, 293.6 | 66.7, 91.8 | 125.6, 133.9 | 142.6, 80.7 | 40.0, 69.1 |
| Solvent content (%) | 68.3 | 67.8 | 65.0 | 74.0 | 68.6 | 54.7 |
| Mean mosaicity (°) | 0.04 | 0.04 | 0.07 | 0.04 | 0.03 | 0.15 |
| Resolution range (Å) | 46–2.54 (2.60–2.54) | 48–2.30 (2.40–2.30) | 50–2.10 (2.18–2.10) | 50–2.15 (2.21–2.15) | 49.06–2.50 (2.60–2.50) | 23–1.55 (1.59–1.55) |
| Total No. of reflections | 176105 (9374) | 232642 (32937) | 45307 (4574) | 1095436 (85346) | 102820 (11312) | 21681 (605) |
| No. of unique reflections | 23922 (1598) | 34862 (4066) | 12281 (1196) | 57690 (4522) | 31982 (3668) | 5485 (304) |
| Completeness (%) | 90.6 (84.6) | 99.5 (100.0) | 97.2 (98.3) | 98.5 (99.6) | 98.5 (98.9) | 91.5 (69.7) |
| Multiplicity | 7.5 (6.0) | 6.7 (8.1) | 3.7 (3.8) | 19.0 (18.9) | 3.2 (3.1) | 3.9 (2.0) |
| 〈I/σ(I)〉 | 8.1 (1.3) | 6.9 (0.7) | 11.3 (1.8) | 12.0 (1.4) | 6.3 (0.8) | 6.1 (1.8) |
| R meas (%) | 18.9 (126.0) | 18.0 (231.2) | 7.5 (84.7) | 17.4 (206.4) | 8.6 (86.8) | 17.9 (45.6) |
| CC1/2 (%) | 98.7 (55.0) | 98.7 (46.9) | 99.7 (73.5) | 99.7 (69.4) | 99.4 (49.4) | 98.8 (75.5) |
| B factor from Wilson plot (Å2) | 57.4 | 60.6 | 45.2 | 50.8 | 63.3 | 23.6 |
| Reflections in working/test sets | 23583/1180 | 34840/3405 | 11053/1228 | 57659/5758 | 31516/1573 | 5484/382 |
| Final R work/R free (%) | 18.8/21.4 | 20.0/22.9 | 16.9/21.1 | 16.2/18.4 | 17.2/19.9 | 19.2/22.3 |
| No. of non-H atoms | ||||||
| Total | 2998 | 3028 | 970 | 4017 | 4446 | 390 |
| Protein | 2989 | 2989 | 947 | 3921 | 4404 | 342 |
| Solvent | 9 | 10 | 23 | 96 | 47 | 43 |
| Ligand | 0 | 29 | 0 | 0 | 33 | 0 |
| Ion | 0 | 0 | 0 | 0 | 2 | 5 |
| R.m.s.d., bonds (Å) | 0.009 | 0.010 | 0.008 | 0.012 | 0.004 | 0.004 |
| R.m.s.d., angles (°) | 1.23 | 1.22 | 0.897 | 1.43 | 1.08 | 0.680 |
| Average B factors (Å2) | ||||||
| Overall | 60.1 | 62.6 | 53.8 | 57.1 | 83.8 | 17.8 |
| Biomolecule | 60.1 | 60.1 | 53.8 | 57.1 | 82.9 | 17.6 |
| Solvent | 52.7 | 55.5 | 50.9 | 56.1 | 62.6 | 15.1 |
| Ramachandran plot regions (%) | ||||||
| Most favored | 98.1 | 97.2 | 95.8 | 98.4 | 96.6 | |
| Allowed | 1.9 | 2.8 | 4.2 | 1.6 | 3.2 | |
| PDB code | 6ibp | 6q52 | 6gzp | 6q3t | 6hw1 | 6ibq |
| PDB code at 100 K† | 6qy6 | 6qxn | 5lmw | 6hf6 | 4zgb | 485d |
| R.m.s. distance (Å2)/ΔV c (%)† | 0.79/5.0 | 0.83/3.8 | 0.79/6.6 | 0.47/4.3 | 1.0/3.9 | 0.40/2.7 |
†
Structures solved at room temperature (this work) are compared with equivalent structures determined at cryogenic temperatures (100 K). R.m.s. distances are calculated taking into account all biomolecule atoms and ΔV c quantifies the increase in the unit-cell volume (V c) at room temperature.