8GPD
Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL18U1 |
Synchrotron site | SSRF |
Beamline | BL18U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-28 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97915 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 39.140, 79.050, 134.280 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 35.080 - 1.400 |
R-factor | 0.1258 |
Rwork | 0.124 |
R-free | 0.15990 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4rl2 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.131 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX (1.19.1_4122) |
Refinement software | PHENIX (1.19.1_4122) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 35.080 | 1.420 |
High resolution limit [Å] | 1.400 | 1.400 |
Number of reflections | 79892 | 17119 |
<I/σ(I)> | 16.32 | |
Completeness [%] | 96.2 | |
Redundancy | 10.2 | |
CC(1/2) | 0.997 | 0.897 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 0.1M Succinate pH5.5, 32%PEG3350 |