9HDM
Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa in complex with thymidine
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ESRF BEAMLINE BM07 |
| Synchrotron site | ESRF |
| Beamline | BM07 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2024-02-01 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9798 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 57.983, 108.293, 115.732 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 40.960 - 1.550 |
| R-factor | 0.1758 |
| Rwork | 0.174 |
| R-free | 0.20070 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.844 |
| Data reduction software | autoPROC |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX ((1.20.1_4487: ???)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 115.730 | 1.580 |
| High resolution limit [Å] | 1.550 | 1.550 |
| Rmerge | 0.087 | 2.827 |
| Rmeas | 0.090 | 2.939 |
| Rpim | 0.025 | 0.799 |
| Total number of observations | 1406879 | 70054 |
| Number of reflections | 106321 | 5222 |
| <I/σ(I)> | 17.1 | 1 |
| Completeness [%] | 100.0 | |
| Redundancy | 13.2 | 13.4 |
| CC(1/2) | 1.000 | 0.535 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 25 % (w/v) PEG 3350, 0.2 M MgCl2 x 6 H2O and 0.1 M HEPES at pH 7.5; Co-crystallized with 15 mM thymidine |
