TABLE 3.
Statistics of diffraction data and structure refinement
| ChiNCTU2: Zn-MAD |
Native with zinc PDB 3N12 | Native without zinc PDB 3N11 | D143A + (NAG)2 PDB 3N13 | 2E145Q + (NAG)2 PDB 3N15 | E145Q/Y227F + (NAG)2 PDB 3N17 | E145G/Y227F + (NAG)4 PDB 3N18 | E145G/Y227F + cyclo-(l-His-LPro) PDB 3N1A | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Peak | Inflection | High-remote | ||||||||
| Data collection | ||||||||||
| Wavelength (Å) | 1.28228 | 1.28284 | 1.25233 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
| Temperature (K) | 110 | 110 | 110 | 110 | 110 | 110 | 110 | 110 | 110 | 110 |
| Space group | P21 | P21 | P21 | P21 | P212121 | P212121 | P212121 | P212121 | P212121 | P212121 |
| Cell dimensions (Å) | ||||||||||
| a | 50.76 | 50.76 | 50.77 | 50.82 | 48.52 | 48.72 | 48.54 | 48.64 | 48.68 | 48.74 |
| b | 48.61 | 48.61 | 48.62 | 48.75 | 76.05 | 76.75 | 76.19 | 76.36 | 75.07 | 75.22 |
| c | 66.63 | 66.6 | 66.64 | 66.65 | 76.61 | 78.5 | 76.31 | 76.91 | 79.41 | 79.45 |
| β | 99.10 | 99.09 | 99.10 | 98.89 | ||||||
| Resolution range (Å)a | 30–2.3 (2.38–2.3) | 30–2.3 (2.38–2.3) | 30–2.24 (2.32–2.24) | 30–1.1 (1.16–1.1) | 30–1.35 (1.40–1.35) | 30–1.7 (1.76–1.7) | 30–1.94 (2.01–1.94) | 30–1.2 (1.24–1.2) | 30–1.6 (1.66–1.6) | 30–2.0 (2.07–2.0) |
| Completeness (%)a | 99.9 (99.7) | 99.9 (99.3) | 99.5 (95.2) | 94.5 (91.3) | 98.8 (96.5) | 99.9 (100) | 99.1 (99.9) | 97.2 (88.1) | 98.2 (96.9) | 99.9 (99.9) |
| Redundancya | 7.4 (7.3) | 7.4 (7.2) | 7.4 (7.1) | 2.6 (2.6) | 5.9 (5.5) | 3.7 (3.6) | 4.8 (5.2) | 6.6 (5.2) | 6.2 (6.3) | 6.6 (7.0) |
| 〈I/σ(I)〉a | 20.4 (8.3) | 28.5 (11.42) | 27.1 (10.69) | 16.5 (2.95) | 34.7 (6.2) | 24.1 (3.6) | 20.2 (11.3) | 43.3 (8.5) | 39.5 (5.6) | 27.35 (6.09) |
| Rsym(%)a,b | 9.5 (26.0) | 6.9 (18.2) | 7.1 (19.1) | 5.5 (42.7) | 4.9 (28.0) | 5.3 (37.5) | 6.5 (15.0) | 4.7 (19.9) | 4.5 (33.3) | 7.5 (42.4) |
| Refinement | ||||||||||
| Resolution range (Å) | 30–1.2 | 30–1.35 | 30–1.7 | 30–1.94 | 30–1.2 | 30–1.6 | 30–2.0 | |||
| Rworkc/Rfreed (%) | 19.8/21.3 | 20.2/21.5 | 18.6/21.0 | 18.0/22.2 | 17.5/18.7 | 19.7/22.7 | 19.9/23.7 | |||
| No. of atoms | ||||||||||
| Protein | 2558 | 2501 | 2506 | 2509 | 2534 | 2511 | 2511 | |||
| Ligand/ion | 8 | 29 | 29 | 29 | 57 | 17 | ||||
| Water molecules | 302 | 342 | 146 | 191 | 291 | 321 | 96 | |||
| B-factors (Å2) | ||||||||||
| Protein | 11.12 | 11.90 | 15.76 | 18.76 | 7.39 | 16.1 | 27.6 | |||
| Ligand/ion | 31.54 | 19.08 | 19.29 | 8.58 | 48.4 | 60.0 | ||||
| Water molecules | 20.21 | 25.25 | 22.87 | 26.10 | 15.84 | 30.6 | 30.8 | |||
| Root mean square deviations | ||||||||||
| Bond lengths (Å) | 0.0034 | 0.0047 | 0.0057 | 0.0067 | 0.0042 | 0.0044 | 0.0033 | |||
| Bond angles (°) | 0.8934 | 0.9376 | 1.0034 | 1.1713 | 0.9803 | 0.9669 | 0.7548 | |||
a Values in parentheses are for highest resolution shells.
b Rsym = ΣhΣi [|Ii (h) − 〈I(h)〉|/ΣhΣiIi(h)], where Ii is the ith measurement, and 〈I(h)〉 is the weighted mean of all measurements of I(h).
c Rwork = Σh|Fo − Fc|/ΣhFo, where Fo and Fc are the observed and calculated structure factor amplitudes of reflection h.
d Rfree is as Rwork but calculated with 10% of randomly chosen reflections omitted from refinement.