5YE9
The crystal structure of Lp-PLA2 in complex with a novel inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17U1 |
Synchrotron site | SSRF |
Beamline | BL17U1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-01-09 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.9791 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 115.091, 83.612, 96.601 |
Unit cell angles | 90.00, 114.90, 90.00 |
Refinement procedure
Resolution | 29.736 - 1.876 |
R-factor | 0.1686 |
Rwork | 0.167 |
R-free | 0.20080 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5i8p |
RMSD bond length | 0.007 |
RMSD bond angle | 1.071 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.29) |
Refinement software | PHENIX ((phenix.refine: 1.9_1692)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 87.620 | 87.620 | 1.980 |
High resolution limit [Å] | 1.876 | 5.930 | 1.880 |
Rmerge | 0.154 | 0.056 | 1.105 |
Rmeas | 0.166 | 0.061 | 1.187 |
Rpim | 0.061 | 0.023 | 0.432 |
Number of reflections | 66597 | 2198 | 9924 |
<I/σ(I)> | 10.6 | ||
Completeness [%] | 97.9 | 98.6 | 100 |
Redundancy | 7.3 | 6.9 | 7.5 |
CC(1/2) | 0.997 | 0.996 | 0.718 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.1M MOPS pH 6.6, 0.4M Li2SO4, 27% (w/v) (NH4)2SO4, 1M Na-Ac, 1.4% 1,4-butanediol |