5CLD
Alkylpurine DNA glycosylase AlkD bound to DNA containing an oxocarbenium-intermediate analog and a free 3-methyladenine nucleobase
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 21-ID-F |
| Synchrotron site | APS |
| Beamline | 21-ID-F |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2014-08-02 |
| Detector | MARMOSAIC 225 mm CCD |
| Wavelength(s) | 0.97872 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 38.202, 92.826, 48.309 |
| Unit cell angles | 90.00, 113.71, 90.00 |
Refinement procedure
| Resolution | 34.979 - 1.541 |
| R-factor | 0.1508 |
| Rwork | 0.149 |
| R-free | 0.17920 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 3bvs |
| RMSD bond length | 0.006 |
| RMSD bond angle | 1.049 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | PHENIX |
| Refinement software | PHENIX |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.000 | 50.000 | 1.570 |
| High resolution limit [Å] | 1.540 | 4.180 | 1.540 |
| Rmerge | 0.057 | 0.036 | 0.255 |
| Rmeas | 0.062 | 0.038 | 0.277 |
| Rpim | 0.023 | 0.014 | 0.105 |
| Total number of observations | 313407 | ||
| Number of reflections | 44235 | ||
| <I/σ(I)> | 14.9 | 6.902 | |
| Completeness [%] | 97.2 | 97.5 | 92.2 |
| Redundancy | 7.1 | 7.4 | 6.4 |
| CC(1/2) | 0.999 | 0.972 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.7 | 294 | 19% w/v PEG4000, 42 mM sodium acetate, pH 4.6, 85 mM ammonium acetate, 5% v/v glycerol |
