6LJ8
Crystal structure of NDM-1 in complex with D-captopril derivative wss04134
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17U1 |
Synchrotron site | SSRF |
Beamline | BL17U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-12-01 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97918 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 41.451, 59.861, 41.956 |
Unit cell angles | 90.00, 98.05, 90.00 |
Refinement procedure
Resolution | 31.500 - 1.400 |
R-factor | 0.144 |
Rwork | 0.143 |
R-free | 0.16720 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5xp6 |
RMSD bond length | 0.007 |
RMSD bond angle | 1.501 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.450 |
High resolution limit [Å] | 1.400 | 3.020 | 1.400 |
Rmerge | 0.060 | 0.056 | 0.177 |
Rmeas | 0.065 | 0.061 | 0.198 |
Rpim | 0.025 | 0.024 | 0.088 |
Total number of observations | 252345 | ||
Number of reflections | 39834 | 4041 | 3935 |
<I/σ(I)> | 26.3 | ||
Completeness [%] | 99.9 | 99.2 | 99.9 |
Redundancy | 6.3 | 6.6 | 4.8 |
CC(1/2) | 0.996 | 0.963 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 295 | 0.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline |