Extended Data Table 2 ∣.
Crystal data, data collection and structure refinement details.
| Protein | A3A-E72A TTC-hairpin | A3A-E72 (no Zn2+) TTC-hairpin | A3A-E72A ATTC-hairpin | A3A-E72A CTTC-hairpin | A3A-wt/TTFdZ-hairpin (form 1) | A3A-wt TTFdZ-hairpin (form 2) |
|---|---|---|---|---|---|---|
| Ligand | 5′T(GC)2TTC(GC)2T | 5′T(GC)2TTC(GC)2T | 5′C3ATCATTCGATG3 | 5′GC2GACCTTCGTCG2G | 5′T(GC)2TTFdZ(GC)2T | 5′T(GC)2TTFdZ(GC)2T |
| PDB ID | 8FIM | 8FIL | 8FIK | 8FII | 8FIJ | |
| Crystal data | ||||||
| Beamline (Temp.) dataset # |
MX2 (100 K) #131 |
MX2 (100 K) #250r |
MX2 (100 K) #84 |
MX2 (100 K) #231 |
MX2 (100 K] #339 |
MX2 (100 K) #106+#108 |
| α (/Å) | 53.92 | 54.75 | 55 | 53.35 | 49.94 | 53.32 |
| b (/Å) | 56.9 | 57.35 | 57.23 | 56.74 | 56.37 | 57.2 |
| c (/Å) | 91.55 | 93.74 | 92.75 | 93.27 | 90.11 | 91.42 |
| β (/°) | 103.6 | 105.8 | 106.5 | 106.24 | 104 | 99.37 |
| Crystal habit | Flattened needle | Thin plate | Flattened needle | Flattened needle | Flattened needle <1×2×5 mm | Flattened needle <1×2×5 mm |
| Crystal system | Monoclinic | Monoclinic | Monoclinic | Monoclinic | Monoclinic | Monoclinic |
| Space group | P21 | P21 | P21 | P21 | P21 | P21 |
| Z′ | 2 | 2 | 2 | 2 | 2 | 2 |
| Data collection | MX2 (Australian Synchrotron) – 1 microfocus 10×5 mm | |||||
| Resolution [highest] | 47.94-2.22 [2.29-2.22] | 48.40-2.10 [2.15-2.10] | 48.13-1.91 [1.96-1.91] | 47.93-3.15 [3.36-3.15] | 48.24-2.80 [2.95-2.80] | 49.05-2.94 [3.12-2.94] |
| # reflections | 89 061 [6814] | 102 081 [6311] | 142 158 [8859] | 31 403 [4962] | 39 433 [5461] | 45 891 [7086] |
| # unique reflns | 26 243 [2098] | 36 510 [2435] | 42 309 [2706] | 9310 [1573] | 11861 [1629] | 11619 [1817] |
| # reflns for Rfree | 1309 | 1622 | 2103 | 520 | 623 | 567 |
| Redundancy | 3.4 [3.2] | 2.8 [2.6] | 3.4 [3.3] | 3.4 [3.2] | 33 [3.4] | 3.9 [3.9] |
| Completeness | 97.3 [85.1] | 97.8 [88.3] | 98.4 [94.2] | 98.3 [92.9] | 97.8 [92.8] | 99.0 [97.1] |
| R merge | 0.092 [1.535] | 0.113 [1.294] | 0.090 [0.913] | 0.342 [1.158] | 0.183 [1.157] | 0.166 [0.583] |
| R pin | 0.059 [0.979] | 0.081 [0.955] | 0.057 [0.589] | 0.218 [0.769] | 0.118 [0.735] | 0.094 [0.338] |
| CC 1/2 | 0.995 [0.332] | 0.992 [0.188] | 0.996 [0.471] | 0.962 [0.621] | 0.979 [0.466] | 0.985 [0.918] |
| I/σ(I) | 6.2 [0.6] | 6.1 [0.7] | 7.5 [1.0] | 2.8 [1.0] | 4.5 [0.8] | 5.8 [2.2] |
| Mosaicity (/°) | 0.37 | 0.15 | 0.08 | 0.34 | 0.28 | 0.33 |
| Wilson B (/Å2) | 51 | 38.2 | 26.3 | 52.8 | 57 | 42.3 |
| Structure refinement | ||||||
| Resolution [highest] | 47.94-2.22 [2.28-2.22] | 40.94-2.10a [2.16-2.10] | 48.17-1.91 [1-96-1.91] | 47.98-3.15 [3.23-3.15] | 48.29-2.80 [2.87-2.80] | 48.35 [2.94] [3.02-2.94] |
| R work | 0.233 [0.369] | 0.228 [0.377]a | 0.201 [0.0.308] | 0.304 [0.433] | 0.260 [0.364] | 0.252 [0.385] |
| R free | 0.274 [0.411] | 0.265 [0.338]a | 0.233 [0.302] | 0.350 [0.438] | 0.323 [0.370] | 0.314 [0.356] |
| # atoms (total) | 3616 | 3712 | 3915 | 3392 | 3325 | 3368 |
| # protein atoms | 3045 | 2939 | 3098 | 2926 | 2926 | 2884 |
| # nucleotide atoms | 520 | 520 | 614 | 447 | 164+202 | 224+224 |
| # other atoms | 2×I6P, 2×(½) Zn2+, 2×Cl− | 2×I6P, 2×Cl−, no Zn2+ | 1×PO4, 1xI6P, 2×Zn2+, 2×Cl− | 3×PO4,a 2×Zn2+, 2×Cl− | 6×PO43−, a 2×Zn2+ | 7×PO43−, a 2×Zn2+ |
| # water molecules | 11 | 78 | 147 | 0 | 2 | |
| Wilson B (/Å2) | 57.2 | 24.6 | 26.3 | 59.9 | 50.2 | 443 |
| Rmsd bond distances [/Å] | 0.006 | 0.008 | 0.01 | 0.005 | 0.008 | 0.007 |
| Rmsd bond angles (/°) | 1.58 | 1.84 | 1.9 | 1.26 | 1.65 | 1.57 |
| Ramachandran (COOT) | ||||||
| OK/OK-ish/Bad (/%) | 91.9/6.5/1.6 | 94.1/5.6/0.3 | 94.8/5.2/0.0 | 92.2/6.8/1.1 | 97.5/1.4/1.1 | 97.7/17/0.6 |
a
Lilely a partially occupied and somewhat disordered ISP (inositol hexaphospliate).