6XVJ
Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I03 |
| Synchrotron site | Diamond |
| Beamline | I03 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2015-08-01 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.97626 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 51.724, 56.257, 60.260 |
| Unit cell angles | 90.00, 110.40, 90.00 |
Refinement procedure
| Resolution | 48.480 - 1.780 |
| R-factor | 0.18 |
| Rwork | 0.178 |
| R-free | 0.21500 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | internal model |
| RMSD bond length | 0.010 |
| RMSD bond angle | 0.990 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.5.12) |
| Phasing software | AMoRE |
| Refinement software | BUSTER |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 56.480 | 56.480 | 1.880 |
| High resolution limit [Å] | 1.780 | 5.630 | 1.780 |
| Rmerge | 0.042 | 0.025 | 0.490 |
| Rmeas | 0.050 | 0.030 | 0.587 |
| Rpim | 0.027 | 0.017 | 0.319 |
| Total number of observations | 93735 | 3235 | 14778 |
| Number of reflections | 29228 | 1033 | 4533 |
| <I/σ(I)> | 15.4 | 39 | 2.3 |
| Completeness [%] | 93.5 | 99.2 | 99.9 |
| Redundancy | 3.2 | 3.1 | 3.3 |
| CC(1/2) | 0.999 | 0.998 | 0.801 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 8.5 | 293 | 25 % PEG550MME, 0.1 M NaCl, 0.1 M TRIS buffer pH 8.5 |
