TABLE 2.
Crystal data and refinement parameters for the ternary (protein·DNA·dGTP) complexes of Dpo4
| Parameter | Npg-1 | Npg-2 |
|---|---|---|
| Data collection | ||
| X-ray source | APS (LS-CAT) | APS (SER-CAT) |
| Beam line | ID-21 | ID-22 |
| Detector | MAR CCD | MAR CCD |
| Wavelength (Å) | 0.98 | 0.99 |
| Temperature (K) | 110 | 110 |
| Number of crystals | 1 | 1 |
| Space group | P21212 | P21212 |
| Unit cell (a, b, c; Å) | 95.04, 103.91, 52.32 | 95.92, 103.83, 52.49 |
| Resolution range (Å) | 19.97-3.10 | 29.25-3.0 |
| Highest resolution shella | (3.19-3.10) | (3.19-3.0) |
| Number of measurements | 63,806 (6,312) | 78,594 (1,746) |
| Number of unique reflections | 9,733 (912) | 11,751 (1,607) |
| Redundancy | 6.5 (6.9) | 6.6 (7.3) |
| Completeness (%) | 98.4 (95.1) | 98.5 (97.1) |
| Rmergeb | 9.4 (64.9) | 7.8 (60.7) |
| Signal to noise (〈I/σI〉) | 15.68 (3.22) | 23.37 (4.70) |
| Solvent content (%) | 56.3 | 59.5 |
| Model composition (asymmetric unit) | ||
| Number of amino acid residues | 342 | 342 |
| Number of water molecules | 42 | |
| Number of Mg2+ ions | 4 | 4 |
| Number of template nucleotides | 16 | 16 |
| Number of primer nucleotides | 14 | 14 |
| Number of dGTP | 1 | 1 |
| Rfc (%) | 23.3 | 22.6 |
| Rfreed (%) | 28.2 | 28.2 |
| Estimated coordinate error (Å) | ||
| From Luzatti plot | 0.45 | 0.40 |
| From Luzatti plot (c-ve) | 0.59 | 0.54 |
| From σA plot | 0.54 | 0.36 |
| From σA plot (c-v) | 0.79 | 0.50 |
| Temperature factors | ||
| From Wilson plot (Å2) | 62.4 | 57.3 |
| Mean isotropic (Å2) | 88.9 | 77.4 |
| r.m.s.d. in temperature factors | ||
| Bonded main-chain atoms (Å2) | 1.25 | 1.50 |
| Bonded side-chain atoms (Å2) | 1.53 | 2.25 |
| r.m.s.d. from ideal values | ||
| Bond lengths (Å) | 0.009 | 0.009 |
| Bond angles (°) | 1.6 | 1.6 |
| Dihedral angles (°) | 22.8 | 22.2 |
| Improper angles (°) | 1.96 | 1.77 |
a
Values in parentheses correspond to the highest resolution shells.
b
Rmerge = Σhkl Σj = 1,N |〈Ihkl〉 — Ihklj|/Σhkl Σj = 1,N|Ihklj|, where the outer sum (hkl) is taken over the unique reflections.
c
Rf = Σhkl Fohkl|—k|Fchkl/Σhkl|Fohkl|, where |Fohkl| and |Fchkl| are the observed and calculated structure factor amplitudes, respectively.
d
Rfree idem, for the set of reflections (5% of the total) omitted from the refinement process.
e
c-v, cross-validation.