6XCI
Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-3D
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 5.0.1 |
Synchrotron site | ALS |
Beamline | 5.0.1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-12-04 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97741 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 71.168, 73.789, 77.654 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.800 - 1.600 |
R-factor | 0.1381 |
Rwork | 0.137 |
R-free | 0.15980 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4exs |
RMSD bond length | 0.013 |
RMSD bond angle | 1.694 |
Data reduction software | xia2 |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 42.800 | 42.760 | 1.630 |
High resolution limit [Å] | 1.600 | 8.760 | 1.600 |
Rmerge | 0.054 | 0.035 | 0.377 |
Rmeas | 0.059 | 0.038 | 0.507 |
Rpim | 0.023 | 0.015 | 0.337 |
Total number of observations | 2305 | 1124 | |
Number of reflections | 49546 | 400 | 831 |
<I/σ(I)> | 19.9 | 40.6 | 2.1 |
Completeness [%] | 90.6 | 99.4 | 31.2 |
Redundancy | 5.5 | 5.8 | 1.4 |
CC(1/2) | 0.999 | 0.999 | 0.797 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 22% PEG 2000 monomethyl ether, 0.1M MES, pH 6.5 and 200mM NaCl) |