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
| 実験手法 | 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 |
| 格子定数 [Å] | 158.949, 158.949, 90.594 |
| 格子定数 [度] | 90.00, 90.00, 120.00 |
精密化法
| 残基 | 34.163 - 3.000 |
| R因子 | 0.2173 |
| Rwork | 0.216 |
| R-free | 0.24830 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5ceh |
| 結合長の平均二乗偏差(RMSD) [Å] | 0.008 |
| 結合角の平均二乗偏差(RMSD) [度] | 0.940 |
| Data reduction software | HKL-2000 |
| Data scaling software | SCALEPACK |
| Phasing software | PHASER |
| Refinement software | PHENIX |
Quality characteristics
| Overall | Inner shell | Outer shell | |
| 分解能 [Å] (低) | 35.000 | 35.000 | 3.050 |
| 分解能 [Å] (高) | 3.000 | 8.110 | 3.000 |
| Rmerge_l_obs | 0.084 | 0.023 | 0.812 |
| Rmeas | 0.090 | 0.025 | 0.875 |
| Rpim | 0.031 | 0.009 | 0.324 |
| 独立反射数 | 26796 | ||
| <I/σ(I)> | 8.5 | ||
| 完全性 [%] | 100.0 | 99.9 | 100 |
| 冗長性 | 8 | 8 | 7.2 |
| CC(1/2) | 0.999 | 0.654 |
結晶化条件
| 結晶ID | 方法 | pH | 温度 | 溶液条件 |
| 1 | VAPOR DIFFUSION | 7.3 | 291 | 200 uM inhibitor, 20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol |
