4MDZ
Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I04-1 |
| Synchrotron site | Diamond |
| Beamline | I04-1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2013-02-18 |
| Detector | DECTRIS PILATUS 2M |
| Wavelength(s) | 0.9795 |
| Spacegroup name | I 2 2 2 |
| Unit cell lengths | 70.190, 183.010, 233.460 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 65.540 - 2.680 |
| R-factor | 0.18594 |
| Rwork | 0.184 |
| R-free | 0.22780 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 4mcw |
| RMSD bond length | 0.013 |
| RMSD bond angle | 1.717 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | MOLREP |
| Refinement software | REFMAC (5.6.0117) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 66.000 | 2.750 |
| High resolution limit [Å] | 2.680 | 2.680 |
| Rmerge | 0.077 | 0.680 |
| Number of reflections | 42290 | |
| <I/σ(I)> | 14.3 | 1.9 |
| Completeness [%] | 99.4 | 99.6 |
| Redundancy | 4.1 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 0.9 M succinate pH 7, 2% PEG 2000, 0.1 M MES buffer pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
