Table 1.
Data Collection and Refinement Statistics
| Pt Derivativea | APAH-CAPS | APAH-M344 | H159A APAH-N8-Acetylspermidine | H159A APAH-acetylspermine | |
|---|---|---|---|---|---|
| A. Data Collection | |||||
| Incident wavelength (Å) | 1.07197 | 0.97949 | 0.97949 | 0.97949 | 0.97950 |
| Resolution Range (Å) | 50–3.95 | 50.0–2.35 | 50.0–2.25 | 50.0–2.30 | 50–2.50 |
| No. of reflections (total/unique) | 761,867/101,559 | 759,655/235,850 | 978,958/270,384 | 536,321/221,353 | 732,096/190,942 |
| Completenessb (%) | 100 (99.9) | 98.3 (97.6) | 98.4 (97.2) | 98.1 (97.0) | 98.2 (97.2) |
| I/σ | 14.0 (5.31) | 14.5 (2.50) | 14.8 (2.85) | 7.26 (1.94) | 15.7 (2.32) |
| Rmergec | 0.195 (0.383) | 0.099 (0.600) | 0.096 (0.326) | 0.117 (0.382) | 0.093 (0.558) |
| Figure of merit | 0.311 | ||||
| B. Refinement | |||||
| No. of reflections, work/test sets | 209,132/11,007 | 246,244/12,854 | 197,638/21,958 | 162,244/17,918 | |
| Rwork/Rfreed | 0.189/0.225 | 0.171/0.202 | 0.186/0.227 | 0.190/0.230 | |
| Protein atoms | 30,808 | 30,812 | 30,816 | 30,816 | |
| Solvent atoms | 1,394 | 2,243 | 1,752 | 943 | |
| Ligand atoms | 168 | 264 | 156 | 204 | |
| R.m.s. deviations | |||||
| Bonds (Å) | 0.007 | 0.006 | 0.007 | 0.007 | |
| Angles (°) | 1.3 | 1.2 | 1.2 | 1.2 | |
| Dihedral angles (°) | 23.3 | 23.0 | 23.3 | 23.2 | |
| Improper dihedral angles (°) | 0.8 | 0.9 | 0.8 | 0.9 | |
| Average B factors (Å2) | |||||
| Main chain | 37 | 21 | 25 | 37 | |
| Side chain | 38 | 24 | 26 | 38 | |
| Ligand | 90e | 39f | 50g | 67h | |
| Solvent | 38 | 28 | 28 | 32 | |
| Zn2+ ions | 52i | 26 | 75j | 90k | |
| K+ ions (MVCl site 1) | 32 | 16 | 22 | 34 | |
| Na+ ions (MVCl site 2) | 19 | 19 | 21 | 32 | |
| K+ ions (MVCl site 3) | 87 | 42 | |||
| Ramachandran plot | |||||
| Allowed (%) | 88.4 | 89.9 | 88.7 | 87.9 | |
| Additionally allowed (%) | 11.0 | 9.5 | 10.6 | 11.5 | |
| Generously allowed (%) | 0.4 | 0.3 | 0.6 | 0.6 | |
| Disallowed (%) | 0.1 | 0.4 | 0.1 | 0.0 | |
Bijvoet pairs kept separate for these data.
Numbers in parentheses refer to the outer shell of data.
Rmerge = Σ|I-〈I〉|/ΣI, where I is the observed intensity and 〈I〉 is the average intensity calculated from replicate data.
Rwork = Σ| |Fo| -|Fo| |/Σ|Fo| for reflections contained in the working set, and Rfree = Σ| |Fo| -|Fo| |/Σ|Fo| for reflections contained in the test set held aside during refinement. |Fo| and |Fo| are the observed and calculated structure factor amplitudes, respectively.
Values range from 80 Å2 (chain G) to 99 Å2 (chain F).
Values range from 34 Å2 (chain D) to 47 Å2 (chain I).
Values range from 36 Å2 (chain I) to 64 Å2 (chain A).
Values range from 42 Å2 (chain I) to 82 Å2 (chain F).
Values range from 46 Å2 (chain D) to 59 Å2 (chain F).
Values range from 53 Å2 (chain A) to 106 Å2 (chain G).
Values range from 73 Å2 (chain L) to 115 Å2 (chain K).
MVC, monvalent cation site