TABLE 1.
Data collection, refinement, and Ramachandran statistics for SAMHD1c tetramers in the presence of dGTP/dATP, dGTP/dCTP, dGTP/dTTP, dGTP/dUTP, and GTP/dATP substrates
Data were obtained from the best diffracting crystal of SAMHD1c H206R/D207N according to crystallization conditions (see “Experimental Procedures” for details) and collected at −180 °C. Crystallographic phases were solved using molecular replacement based on the SAMHD1c-dGTP/dGTP tetramer model (Protein Data Bank code 4BZB). Refinement was carried out using Phenix. Values in parentheses are for the highest resolution shell.
| SAMHD1c-dGTP/dATP | SAMHD1c-dGTP/dCTP | SAMHD1c-dGTP/dTTP | SAMHD1c-dGTP/dUTP | SAMHD1c-GTP/dATP | |
|---|---|---|---|---|---|
| Data collection | |||||
| Space group | P21 | P21 | P21 | P21 | P21 |
| Cell dimensions | |||||
| a, b, c (Å) | 88.56/147.26/98.80 | 87.97/147.02/98.87 | 87.83/146.74/98.94 | 87.86/146.60/98.69 | 87.70/146.72/99.26 |
| α, β, γ (degrees) | 90/114.63/90 | 90/114.31/90 | 90/114.29/90 | 90/114.62/90 | 90/114.76/90 |
| Asymmetric unit content | 4 | 4 | 4 | 4 | 4 |
| Wavelength (Å) | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| Resolution (Å) | 38.34-2.20 (2.28-2.20) | 38.67-2.10 (2.18-2.10) | 33.98-2.30 (2.38-2.30) | 42.91-2.30 (2.38-2.30) | 42.99-2.20 (2.28-2.20) |
| Rmerge | 0.134 (0.500) | 0.108 (0.495) | 0.090 (0.539) | 0.113 (0.487) | 0.074 (0.505) |
| Rmeas | 0.146 (0.544) | 0.117 (0.531) | 0.101 (0.604) | 0.123 (0.531) | 0.089 (0.605) |
| 〈I/σI〉 | 5.7 (2.1) | 7.0 (2.3) | 8.0 (1.7) | 7.2 (2.3) | 6.8 (1.6) |
| Completeness (%) | 99.9 (100.0) | 99.8 (100.0) | 99.9 (99.8) | 99.8 (100.0) | 99.3 (99.7) |
| Redundancy | 6.38 (6.38) | 7.68 (7.68) | 5.09 (5.01) | 6.46 (6.46) | 3.20 (3.18) |
| Mosaicity | 0.65 | 0.43 | 0.78 | 0.51 | 0.78 |
| Refinement | |||||
| Resolution (Å) | 38.34-2.20 (2.26-2.20) | 38.67-2.10 (2.15-2.10) | 33.98-2.30 (2.36-2.30) | 42.91-2.30 (2.36-2.30) | 42.99-2.20 (2.26-2.20) |
| No. of unique reflections | 116,344 | 132,888 | 101,122 | 100,456 | 114,395 |
| No. of test reflectionsa | 2002 | 2009 | 2013 | 2011 | 2000 |
| Rwork/Rfree | 0.228/0.270 (0.257/0.313) | 0.226/0.269 (0.287/0.325) | 0.209/0.250 (0.338/0.390) | 0.197/0.250 (0.279/0.349) | 0.214/0.264 (0.362/0.374) |
| No. of atoms | |||||
| Protein | 15,753 | 15,756 | 15,798 | 15,768 | 15.739 |
| Ligand/ion | 376 | 368 | 336 | 359 | 372 |
| Water | 386 | 394 | 228 | 182 | 191 |
| Average B-factors (Å2) | |||||
| Protein | 42.78 | 38.23 | 68.49 | 64.62 | 66.04 |
| Ligand/ion | 32.00 | 29.63 | 48.69 | 44.41 | 53.20 |
| Water | 40.75 | 26.16 | 46.65 | 26.81 | 58.97 |
| Wilson B (Å2) | 41.64 | 39.06 | 46.35 | 46.88 | 53.00 |
| Root mean square deviations | |||||
| Bond lengths (Å) | 0.005 | 0.005 | 0.005 | 0.007 | 0.006 |
| Bond angles (degrees) | 0.979 | 0.971 | 0.953 | 1.070 | 1.146 |
| MolProbity statisticsb | |||||
| All atom clashscore | 8.99 | 7.14 | 7.50 | 6.83 | 6.20 |
| Rotamer outliers (%) | 2.04 | 2.86 | 2.21 | 2.10 | 1.11 |
| Cβ deviation | 4 | 4 | 4 | 5 | 0 |
| Ramachandranb | |||||
| Favored region (%) | 96.44 | 97.02 | 95.88 | 97.13 | 96.33 |
| Allowed region (%) | 3.29 | 2.98 | 4.02 | 2.77 | 3.40 |
| Outliers (%) | 0.26 | 0.00 | 0.10 | 0.10 | 0.26 |
| PDB accession code | 4QFX | 4QFY | 4QFZ | 4QG0 | 4QG1 |
a Random selection.
b Values were obtained from MOLPROBITY.