3DKU
Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PHOTON FACTORY BEAMLINE BL-6A |
| Synchrotron site | Photon Factory |
| Beamline | BL-6A |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2008-05-23 |
| Detector | ADSC QUANTUM 4 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 68.960, 70.521, 145.031 |
| Unit cell angles | 90.00, 103.30, 90.00 |
Refinement procedure
| Resolution | 33.560 - 2.690 |
| R-factor | 0.196 |
| Rwork | 0.193 |
| R-free | 0.27000 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2b0v |
| RMSD bond length | 0.018 |
| RMSD bond angle | 1.848 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.2.0019) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.800 |
| High resolution limit [Å] | 2.690 | 2.690 |
| Rmerge | 0.093 | 0.245 |
| Number of reflections | 37388 | |
| <I/σ(I)> | 18.8 | 5.9 |
| Completeness [%] | 98.8 | 99.7 |
| Redundancy | 2.9 | 2.9 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | 4 | 283 | 0.1 M Citric acid pH 4.0, 3.5% w/v PEG 4000, 0.064 M Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
