5V9P
Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone (compound 35) in complex with KDM5A
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 193 |
Detector technology | CCD |
Collection date | 2014-04-09 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.9787 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 158.949, 158.949, 90.594 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 34.163 - 3.000 |
R-factor | 0.2173 |
Rwork | 0.216 |
R-free | 0.24830 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5ceh |
RMSD bond length | 0.008 |
RMSD bond angle | 0.940 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Phasing software | PHASER |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 35.000 | 35.000 | 3.050 |
High resolution limit [Å] | 3.000 | 8.110 | 3.000 |
Rmerge | 0.084 | 0.023 | 0.812 |
Rmeas | 0.090 | 0.025 | 0.875 |
Rpim | 0.031 | 0.009 | 0.324 |
Number of reflections | 26796 | ||
<I/σ(I)> | 8.5 | ||
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 8 | 8 | 7.2 |
CC(1/2) | 0.999 | 0.654 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 7.3 | 291 | 200 uM inhibitor, 20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol |