TABLE 1.
Data collection and refinement statistics for ZIKV RdRp crystals
| Parametera | Value(s) for the following combinationb
: |
||||
|---|---|---|---|---|---|
| ZRDRP-Apo | ZRDRP-Cpd7 | ZRDRP-Cpd13 | ZRDRP-Cpd14 | ZRDRP-Cpd15 | |
| PDB accession no. | 6LD1 | 6LD2 | 6LD3 | 6LD4 | 6LD5 |
| Data collection statistics | |||||
| Wavelength | 0.9999 | 0.9538 | 0.9538 | 0.9538 | 1.542 |
| Resolution range (Å) | 19.69–1.4 (1.45–1.4) | 55.65–1.4 (1.45–1.4) | 51.18–2.3 (2.38–2.3) | 21.91–1.5 (1.55–1.5) | 34.18–1.94 (2.01–1.94) |
| Space group | P21 | P21 | P21 | P21 | P21 |
| Unit cell dimensions | |||||
| a, b, c (Å) | 64.03, 82.89, 69.43 | 63.94, 85.06, 69.74 | 63.65, 84.99, 69.78 | 64.1, 85.17, 69.81 | 63.47, 84.59, 69.15 |
| α, β, γ (°) | 90, 114.52, 90 | 90, 113.44, 90 | 90, 113.28, 90 | 90, 113.34, 90 | 90, 113.9, 90 |
| No. of reflections | |||||
| Measured | 868,128 (82,587) | 409,259 (30,450) | 105,406 (10,139) | 350,892 (29,638) | 132,120 (7,631) |
| Unique | 126,423 (12,347) | 132,763 (13,223) | 29,894 (2,928) | 109,191 (10,777) | 46,894 (4,079) |
| Multiplicity | 6.9 (6.7) | 3.1 (2.3) | 3.5 (3.5) | 3.2 (2.8) | 2.8 (1.9) |
| Completeness (%) | 97.54 (95.46) | 98.72 (98.27) | 98.15 (97.18) | 99.23 (98.44) | 95.88 (84.16) |
| Mean I/sigma〈I〉 | 15.95 (0.93) | 13.06 (0.69) | 10.22 (1.75) | 11.84 (0.59) | 5.89 (1.41) |
| Refinement statistics | |||||
| Wilson B factor (Å2) | 20.79 | 24.83 | 45.33 | 28.32 | 15.94 |
| Rmerge | 0.05486 (1.707) | 0.03512 (0.8589) | 0.08542 (0.6131) | 0.04154 (1.258) | 0.1362 (0.5432) |
| Rmeas | 0.05936 (1.845) | 0.04193 (1.128) | 0.1007 (0.7268) | 0.04953 (1.561) | 0.168 (0.7425) |
| Rpim | 0.02245 (0.6945) | 0.02267 (0.723) | 0.05254 (0.385) | 0.02672 (0.9115) | 0.09655 (0.503) |
| CC1/2 | 0.999 (0.433) | 0.999 (0.419) | 0.997 (0.656) | 0.999 (0.381) | 0.981 (0.534) |
| CC* | 1 (0.777) | 1 (0.769) | 0.999 (0.89) | 1 (0.742) | 0.995 (0.834) |
| No. of reflections used in refinement | 126,423 (12,344) | 132,761 (13,221) | 29,888 (2,928) | 109,190 (10,772) | 46,890 (4,079) |
| No. of reflections used for Rfree | 6,321 (617) | 6,637 (661) | 1,492 (147) | 5,458 (539) | 2,343 (204) |
| Rwork | 0.1962 (0.3212) | 0.2020 (0.3789) | 0.1916 (0.2657) | 0.1964 (0.3560) | 0.1840 (0.2749) |
| Rfree | 0.2182 (0.3260) | 0.2271 (0.3786) | 0.2489 (0.3294) | 0.2238 (0.3833) | 0.2260 (0.3265) |
| CC | |||||
| Work | 0.956 (0.630) | 0.957 (0.597) | 0.931 (0.758) | 0.958 (0.592) | 0.945 (0.717) |
| Free | 0.953 (0.623) | 0.944 (0.659) | 0.968 (0.582) | 0.953 (0.625) | 0.911 (0.704) |
| No. of: | |||||
| Nonhydrogen atoms | 5,314 | 5,347 | 4,989 | 5,434 | 5,463 |
| Macromolecules | 4,834 | 4,709 | 4,745 | 4,693 | 4,742 |
| Ligands | 14 | 20 | 29 | 60 | 64 |
| Solvent atoms | 466 | 618 | 215 | 681 | 657 |
| Protein residues | 574 | 565 | 578 | 565 | 575 |
| RMSD | |||||
| Bond length (Å) | 0.012 | 0.012 | 0.012 | 0.012 | 0.012 |
| Bond angle (°) | 1.47 | 1.50 | 1.52 | 1.45 | 1.47 |
| Ramachandran plot (%) | |||||
| Favored | 98.23 | 97.65 | 97.18 | 97.28 | 97.17 |
| Allowed | 1.77 | 2.17 | 2.82 | 2.54 | 2.83 |
| Outliers | 0.00 | 0.18 | 0.00 | 0.18 | 0.00 |
| Rotamer outliers (%) | 1.54 | 1.39 | 3.54 | 1.39 | 1.38 |
| Clash score | 2.08 | 3.21 | 2.76 | 3.31 | 2.96 |
| B factor | |||||
| Avg | 29.44 | 34.00 | 51.35 | 37.19 | 20.45 |
| Macromolecules | 28.18 | 32.83 | 51.08 | 35.77 | 18.86 |
| Ligands | 38.54 | 30.31 | 86.65 | 38.63 | 31.48 |
| Solvent | 42.18 | 43.00 | 52.69 | 46.86 | 30.90 |
a
I, intensity of a reflection; sigma〈I〉, average intensity; CC1/2, percentage of correlation between intensities from random half data sets; CC*, estimate of correlation of the observed data set with the underlying true signal (33).
b
Statistics for the highest-resolution shell are shown in parentheses. ZRDRP, ZIKV RdRp.