6XVK
Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor bearing an acrylamide
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SOLEIL BEAMLINE PROXIMA 2 |
| Synchrotron site | SOLEIL |
| Beamline | PROXIMA 2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2019-05-30 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.98010 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 51.550, 57.010, 59.890 |
| Unit cell angles | 90.00, 109.73, 90.00 |
Refinement procedure
| Resolution | 48.520 - 1.990 |
| R-factor | 0.208 |
| Rwork | 0.206 |
| R-free | 0.24400 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | internal model |
| RMSD bond length | 0.009 |
| RMSD bond angle | 0.990 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | AMoRE |
| Refinement software | BUSTER |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 48.520 | 48.520 | 2.040 |
| High resolution limit [Å] | 1.980 | 8.880 | 1.980 |
| Rmerge | 0.035 | 0.015 | 1.285 |
| Rmeas | 0.042 | 0.018 | 1.536 |
| Rpim | 0.023 | 0.010 | 0.831 |
| Total number of observations | 75115 | 855 | 4478 |
| Number of reflections | 22301 | 274 | 1393 |
| <I/σ(I)> | 13.5 | 44.3 | 0.7 |
| Completeness [%] | 98.1 | 98.2 | 84.6 |
| Redundancy | 3.4 | 3.1 | 3.2 |
| CC(1/2) | 0.999 | 0.999 | 0.395 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 6.5 | 293 | 11 % PEG8000, 0.1 M PCTP buffer pH 6.5 |
