Table 1 X-ray data collection and refinement statistics.
From: Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase
Complex name | oxoG•dCTP | oxoG•dATP | oxoG•dATP | oxoG•C | oxoG•A |
|---|---|---|---|---|---|
Complex type | insertion | insertion | insertion | extension | extension |
Primer strand 3′ | 2′-deoxy | 2′,3′-dideoxy | 2′-deoxy | 2′-deoxy | 2′-deoxy |
PDB ID | 7JK1 | 7JKL | 7JKP | 7JL8 | 7JLG |
Data collection | |||||
Space group | P1 | P1 | P1 | P1 | P1 |
Cell dimensions: | |||||
a, b, c (Å) | 52.6 65.7 75.2 | 52.5 65.6 74.3 | 52.6 65.7 75.2 | 50.7 65.3 72.0 | 51.0 65.2 73.1 |
α, β, γ (°) | 69.7, 82.8, 88.5 | 69.7, 82.8, 88.5 | 69.7, 82.8, 88.5 | 68.5, 85.7, 86.9 | 71.4, 84.3, 88.6 |
Resolution range (Å)a | 70.0−2.62 (2.74−2.62) | 69.2−2.37 (2.46−2.37) | 69.2−2.58 (2.69−2.58) | 28.2−2.10 (2.16−2.10) | 27.0−2.07 (2.13−2.07) |
Rmerge (%) | 11.2 (122) | 9.2 (91.7) | 8.8 (95.5) | 5.5 (54.3) | 6.1 (108) |
I /σI | 6.1 (0.9) | 7.0 (0.8) | 7.6 (0.7) | 11.6 (1.7) | 8.8 (0.8) |
Completeness (%) | 98.0 (93.9) | 91.2 (64.0) | 94.0 (82.1) | 97.1 (93.6) | 97.0 (95.5) |
Redundancy | 2.1 (2.1) | 3.5 (2.9) | 3.4 (2.7) | 3.4 (3.3) | 3.4 (3.3) |
CC1/2 (%) | 98.8 (36.3) | 99.3 (44.9) | 99.5 (52.3) | 99.8 (78.0) | 99.8 (33.6) |
Refinement | |||||
Resolution range (Å) | 39.5−2.62 (2.71−2.62) | 69.2−2.38 (2.45−2.38) | 69.2−2.58 (2.68−2.58) | 28.2−2.10 (2.15−2.10) | 27.0−2.07 (2.12−2.07) |
No. reflections | 27,566 | 32,954 | 26,648 | 48,566 | 52,522 |
Rwork/Rfree | 23.9/ 28.6 (36.9/ 38.5) | 22.0/ 27.7 (38.6/39.0) | 24.8/ 30.7 (48.1/ 50.0) | 18.7/ 21.3 (29.2/ 32.2) | 20.1/ 21.9 (37.6/ 40.2) |
No. of non-hydrogen atoms | 5,440 | 5,483 | 5,291 | 5,171 | 5,351 |
Protein | 4,122 | 4,159 | 4,053 | 4,085 | 4,116 |
DNA | 1,143 | 1,143 | 1,145 | 807 | 1,021 |
Ligand (dNTP) | 56 | 60 | 60 | 60 | 60 |
Ligand (other) | 25 | 12 | 6 | 55 | 19 |
Ion (Ca2+) | 2 | 3 | 3 | 3 | 4 |
Water | 92 | 106 | 24 | 161 | 131 |
B-factors | |||||
Protein | 64.4 | 66.0 | 76.6 | 52.2 | 61.1 |
DNA | 115.3 | 111.1 | 145.9 | 114.5 | 124.0 |
Ligand (dNTP) | 53.9 | 57.0 | 70.5 | 43.3 | 56.2 |
Ligand (other) | 56.9 | 62.7 | 76.9 | 70.6 | 74.3 |
Ion (Ca2+) | 51.7 | 74.4 | 74.6 | 52.1 | 73.4 |
Water | 54.2 | 60.7 | 63.6 | 48.9 | 54.7 |
R.m.s. deviations | |||||
Bond length (Å) | 0.011 | 0.005 | 0.011 | 0.008 | 0.003 |
Bond angles (°) | 0.681 | 0.497 | 0.495 | 1.011 | 0.647 |
