5Y6E
VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL19U1 |
Synchrotron site | SSRF |
Beamline | BL19U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-07-15 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9785 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 101.355, 74.452, 64.456 |
Unit cell angles | 90.00, 129.46, 90.00 |
Refinement procedure
Resolution | 49.739 - 1.800 |
R-factor | 0.1379 |
Rwork | 0.137 |
R-free | 0.17270 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5lca |
RMSD bond length | 0.022 |
RMSD bond angle | 1.045 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | PHASER (2.6.0) |
Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.600 |
High resolution limit [Å] | 1.570 | 4.260 | 1.570 |
Rmerge | 0.102 | 0.088 | 0.267 |
Rmeas | 0.111 | 0.095 | 0.293 |
Rpim | 0.043 | 0.037 | 0.117 |
Number of reflections | 64049 | 2633 | 2506 |
<I/σ(I)> | 10.2 | ||
Completeness [%] | 99.9 | 99.9 | 99.9 |
Redundancy | 6.4 | 6.6 | 6 |
CC(1/2) | 0.987 | 0.949 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 0.1M Magnesium Formate, 23%-30% (v/v) Polyethylene glycol 3350 |