Table 1.
Data collection and refinement statistics
| Data set ligand | NR3A glycine | NR3A D-serine | NR3A ACPC | NR3B glycine | NR3B D-serine |
|---|---|---|---|---|---|
| Data collection | |||||
| Space group | P21 | P21 | P21 | P212121 | P212121 |
| Unit cell a, b, c (Å) | 49.9, 97.6, 59.9 | 49.8, 97.7, 60 | 49.7, 103.6, 59.8 | 45.9, 83.6, 145.2 | 45.8, 83.5, 145 |
| α, β, γ (deg) | 90, 93.6, 90 | 90, 93.6, 90 | 90, 95, 90 | 90, 90, 90 | 90, 90, 90 |
| Number per a.u. | 2 | 2 | 2 | 2 | 2 |
| Wavelength (Å) | 0.9793 | 1 | 1 | 1 | 1 |
| Resolution (Å)a | 30–1.58 (1.64) | 35–1.45 (1.50) | 30–1.96 (2.03) | 40–1.58 (1.64) | 40–1.62 (1.68) |
| Unique observations | 78 213 | 100 689 | 43 239 | 76 724 | 71 657 |
| Mean redundancyb | 3.8 (3.3) | 3.1 (2) | 2.9 (2.7) | 4.5 (4.2) | 4.5 (4.4) |
| Completeness (%)b | 95.9 (75.3) | 96 (72.1) | 97.9 (96.4) | 92.3 (91.4) | 99 (98.5) |
| Rmerge (%)bb,c | 0.054 (0.255) | 0.050 (0.292) | 0.088 (0.362) | 0.048 (0.326) | 0.052 (0.344) |
| I/σ(I)b | 11.7 (5.6) | 14.3 (2.5) | 8.5 (2.6) | 16.6 (3.2) | 14.5 (4) |
| Refinement | |||||
| Resolution (Å) | 29.89–1.58 | 34.84–1.45 | 19.91–1.96 | 36.30–1.58 | 35.84–1.62 |
| Protein atoms (alt conf) | 4909 (417) | 4823 (325) | 4663 (139) | 4450 (60) | 4471 (84) |
| Ligand atoms | 10 | 14 | 14 | 10 | 14 |
| Glycerol atoms | 24 | 18 | 0 | 6 | 6 |
| Cl/Br atoms | 8 | 3 | 0 | 0 | 0 |
| Water atoms | 631 | 633 | 513 | 527 | 475 |
| Rwork/Rfree (%)d | 14.8/17.7 | 15.3/17.8 | 15.6/21.1 | 19.2/23.1 | 19.2/22.8 |
| RMS deviations | |||||
| Bond lengths (Å) | 0.012 | 0.015 | 0.014 | 0.015 | 0.013 |
| Bond angles (deg) | 1.46 | 1.66 | 1.45 | 1.58 | 1.54 |
| Bonds B-values Mc/Sce | 1.29/1.59 | 1.52/2.01 | 0.86/2.24 | 1.49/1.83 | 1.40/1.74 |
| Angles B-values Mc/Sce | 1.93/2.38 | 2.23/3.02 | 1.38/3.51 | 2.08/2.65 | 1.99/2.47 |
| Mean B-values (Å2) | |||||
| Protein overall | 11.5 | 11.8 | 13.3 | 17.9 | 16.7 |
| Main chain/side chain | 10.4/12.7 | 10.3/13.3 | 12.3/14.3 | 16.6/19.3 | 15.4/18 |
| Ligand | 7.8 | 8.8 | 9.2 | 15.1 | 15.9 |
| Glycerol | 27.3 | 32.1 | — | 29.6 | 29.7 |
| Cl/Br | 25.2 | 32.9 | — | — | — |
| Water | 28 | 30.1 | 28.7 | 33.7 | 33.5 |
| Ramachandran %f | 98.7/0 | 98.7/0 | 98.1/0 | 98.3/0 | 98.3/0 |
| aValues in parentheses indicate the low-resolution limit for the highest resolution shell of data. | |||||
| bValues in parentheses indicate statistics for the highest resolution shell of data. | |||||
| cRmerge= =(Σ∣II−〈II〉∣)/ΣI∣II∣, where 〈II〉 is the mean II over symmetry-equivalent reflections. | |||||
| dRwork=(Σ∣∣Fo∣−∣Fc∣∣)/Σ∣Fo∣, where Fo and Fc denote observed and calculated structure factors, respectively; 5% of the reflections were set aside for the calculation of the Rfree value. | |||||
| eMain chain/side chain. | |||||
| fPreferred/disallowed conformations. | |||||