Table 2. Data-collection and refinement statistics.
Values in parentheses are for highest resolution shell.
| M9–Fe (λZn) | M9–Fe (λFe) | M9–Fe (λMn) | M9–Mn (λZn) | M9–Mn (λFe) | M9–Mn (λMn) | M9–Zn (λZn) | M9–Zn (λFe) | M9–Zn (λMn) | |
|---|---|---|---|---|---|---|---|---|---|
| PDB code | 5uy0 | 5uy4 | 5uy5 | 5uya | 5uyb | 5uyc | 5uyd | 5uye | 5uyf |
| Data collection | |||||||||
| Beamline | CMCF, CLS | CMCF, CLS | CMCF, CLS | CMCF, CLS | CMCF, CLS | CMCF, CLS | CMCF, CLS | CMCF, CLS | CMCF, CLS |
| Wavelength (A) | 1.28215 | 1.74013 | 1.89174 | 1.28215 | 1.74013 | 1.89289 | 1.28215 | 1.74013 | 1.89289 |
| Space group | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 |
| a, b, c (Å) | 61.93, 66.47, 67.25 | 61.93, 66.37, 67.15 | 61.97, 66.49, 67.21 | 41.79, 52.13, 113.01 | 41.75, 52.19, 112.75 | 41.73, 52.18, 112.78 | 41.79, 52.17, 112.80 | 41.81, 52.17, 112.77 | 41.86, 52.19, 112.77 |
| α = β = γ (°) | 90 | 90 | 90 | 90 | 90 | 90 | 90 | 90 | 90 |
| V M † (Å3 Da−1) | 2.22 | 2.22 | 2.23 | 1.98 | 1.97 | 1.97 | 1.98 | 1.98 | 1.98 |
| Solvent content (%) | 44.71 | 44.54 | 44.73 | 37.83 | 37.69 | 37.67 | 37.76 | 37.77 | 37.87 |
| Resolution (Å) | 50.00–1.71 (1.74–1.71) | 50.00–1.92 (1.95–1.92) | 50.00–2.15 (2.19–2.15) | 50.00–1.72 (1.75–1.72) | 50.00–1.95 (1.98–1.95) | 50.00–1.96 (1.99–1.96) | 50.00–1.93 (1.96–1.93) | 50.00–2.09 (2.13–2.09) | 50.00–2.06 (2.10–2.06) |
| Unique reflections | 30412 (1478) | 21484 (1046) | 15410 (654) | 26994 (1320) | 18617 (921) | 18167 (784) | 19305 (937) | 15274 (713) | 15986 (800) |
| Completeness (%) | 98.9 (97.7) | 98.0 (96.1) | 97.5 (85.4) | 99.8 (98.7) | 99.7 (99.9) | 98.9 (88.3) | 99.9 (99.9) | 99.9 (99.9) | 99.9 (99.9) |
| Multiplicity | 8.1 (8.1) | 7.9 (7.8) | 7.8 (6.5) | 7.4 (7.3) | 7.6 (7.5) | 7.3 (4.3) | 7.2 (7.2) | 7.3 (7.4) | 7.2 (6.9) |
| CC1/2 | 99.7 (93.8) | 99.7 (93.4) | 99.7 (95.4) | 99.5 (96.5) | 99.5 (94.1) | 99.6 (74.7) | 99.5 (93.7) | 99.5 (94.1) | 99.5 (88.3) |
| R merge (%) | 8.5 (40.4) | 6.3 (41.4) | 6.5 (24.0) | 9.6 (40.4) | 9.2 (40.2) | 9.4 (37.9) | 9.6 (42.6) | 9.4 (41.8) | 9.3 (41.1) |
| R meas (%) | 9.0 (43.1) | 6.8 (44.3) | 7.0 (26.1) | 10.3 (43.3) | 9.8 (43.3) | 10.1 (43.5) | 10.3 (45.9) | 10.2 (44.9) | 10.0 (44.6) |
| R p.i.m. (%) | 3.2 (15.0) | 2.4 (15.5) | 2.5 (9.9) | 3.7 (15.4) | 3.5 (15.8) | 3.6 (20.8) | 3.8 (16.9) | 3.7 (16.4) | 3.7 (17.1) |
| Mean I/σ(I) | 56.0 (1.4) | 56.0 (3.1) | 67.4 (14.0) | 59.1 (7.9) | 52.7 (5.2) | 73.2 (13.3) | 54.8 (6.4) | 51.3 (6.0) | 67.3 (13.5) |
| Refinement | |||||||||
| Resolution (Å) | 30.97–1.71 (1.73–1.71) | 47.22–1.92 (1.94–1.92) | 37.59–2.14 (2.18–2.14) | 38.32–1.72 (1.74–1.72) | 39.16–1.95 (1.98–1.95) | 38.29–1.96 (1.99–1.96) | 39.19–1.92 (1.95–1.92) | 39.21–2.09 (2.12–2.09) | 38.30–2.06 (2.09–2.06) |
| No. of non-anomalous reflections | 30366 | 21444 | 15376 | 26936 | 21444 | 18116 | 19252 | 15227 | 15934 |
| Completeness (%) | 98.9 (96.5) | 97.8 (89.4) | 97.6 (82.8) | 99.5 (93.9) | 99.5 (96.6) | 98.6 (82.8) | 99.7 (91.9) | 99.9 (97.1) | 99.6 (92.5) |
| R work (%) | 17.85 (23.69) | 17.28 (29.27) | 16.34 (18.19) | 16.45 (18.40) | 16.51 (23.26) | 16.83 (29.84) | 16.19 (22.62) | 16.18 (19.11) | 16.24 (22.29) |
| R free ‡ (%) | 21.24 (23.13) | 20.14 (32.99) | 20.40 (23.83) | 19.22 (21.57) | 20.17 (30.77) | 20.29 (33.45) | 20.11 (28.45) | 20.68 (26.04) | 20.04 (23.20) |
| Wilson B factor (Å2) | 27.603 | 27.43 | 33.109 | 20.66 | 22.293 | 26.003 | 22.727 | 26.184 | 34.315 |
| Average B factor (Å2) | 33.14 | 32.52 | 37.75 | 24.92 | 26.66 | 29.43 | 25.87 | 29 | 37.06 |
| No. of protein atoms | 2133 | 2133 | 2133 | 2153 | 2133 | 2153 | 2153 | 2153 | 2153 |
| Solvent atoms | 285 H2O, 1 Zn | 245 H2O, 1 Fe | 180 H2O, 1 Mn | 293 H2O, 1 Zn | 245 H2O, 1 Fe | 229 H2O, 1 Mn | 284 H2O, 1 Zn | 211 H2O, 1 Fe | 181 H2O, 1 Mn |
| No. of molecules in ASU§ | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| R.m.s.d.¶, bond lengths (Å) | 0.007 | 0.007 | 0.008 | 0.006 | 0.006 | 0.007 | 0.007 | 0.007 | 0.006 |
| R.m.s.d.¶, bond angles (°) | 0.808 | 0.805 | 0.832 | 0.775 | 0.764 | 0.799 | 0.774 | 0.804 | 0.766 |
| Ramachandran plot | |||||||||
| Favored (%) | 98.14 | 98.14 | 98.51 | 96.69 | 98.14 | 96.69 | 96.32 | 96.69 | 97.06 |
| Allowed (%) | 1.86 | 1.86 | 1.49 | 2.21 | 1.86 | 2.57 | 2.94 | 2.57 | 2.21 |
| Outliers (%) | 0 | 0 | 0 | 1.1 | 0 | 0.74 | 0.74 | 0.74 | 0.74 |
| Clashscore | 5.39 | 4.45 | 4.92 | 4.18 | 4.41 | 5.11 | 3.71 | 4.41 | 2.55 |
| MolProbity score | 1.29 | 1.22 | 1.26 | 1.41 | 1.39 | 1.48 | 1.41 | 1.43 | 1.21 |
†
Matthews coefficient.
‡
The test set uses ∼5% of the data.
§
Asymmetric unit.
¶
Root-mean-square deviation.