4OAK
Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU MICROMAX-007 HF |
Temperature [K] | 100 |
Detector technology | IMAGE PLATE |
Collection date | 2013-12-12 |
Detector | RIGAKU RAXIS IV++ |
Wavelength(s) | 1.5418 |
Spacegroup name | P 1 |
Unit cell lengths | 41.939, 43.083, 66.316 |
Unit cell angles | 80.53, 74.52, 64.01 |
Refinement procedure
Resolution | 19.330 - 2.000 |
R-factor | 0.191 |
Rwork | 0.189 |
R-free | 0.23460 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4mur |
RMSD bond length | 0.018 |
RMSD bond angle | 0.810 |
Data reduction software | XDS |
Data scaling software | SCALA |
Phasing software | PHENIX |
Refinement software | PHENIX ((phenix.refine: dev_1538)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 19.330 | 2.110 |
High resolution limit [Å] | 2.000 | 2.000 |
Rmerge | 0.079 | 0.518 |
Number of reflections | 25760 | |
<I/σ(I)> | 11 | 2.3 |
Completeness [%] | 94.9 | 92.3 |
Redundancy | 3.3 | 3.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K, 1 mM CuCl2 and 20 mM D-Ala-D-Ala. Cryoprotectant: paratone, pH 5.6, VAPOR DIFFUSION, HANGING DROP |