6D1Z
Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one Inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I02 |
Synchrotron site | Diamond |
Beamline | I02 |
Temperature [K] | 93 |
Detector technology | PIXEL |
Collection date | 2013-05-09 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 113.150, 45.660, 78.880 |
Unit cell angles | 90.00, 126.88, 90.00 |
Refinement procedure
Resolution | 39.150 - 1.870 |
R-factor | 0.1797 |
Rwork | 0.178 |
R-free | 0.20960 |
RMSD bond length | 0.010 |
RMSD bond angle | 0.950 |
Data reduction software | xia2 |
Data scaling software | Aimless (0.1.27) |
Phasing software | BUSTER |
Refinement software | BUSTER |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 39.150 | 39.150 | 1.920 |
High resolution limit [Å] | 1.870 | 8.360 | 1.870 |
Rmerge | 0.109 | 0.030 | 0.860 |
Rmeas | 0.131 | 0.037 | 1.030 |
Rpim | 0.072 | 0.022 | 0.569 |
Total number of observations | 84657 | ||
Number of reflections | 26217 | 274 | 1963 |
<I/σ(I)> | 9.7 | ||
Completeness [%] | 97.6 | 80.2 | 99.1 |
Redundancy | 3.2 | 2.9 | 3.2 |
CC(1/2) | 0.978 | 0.996 | 0.392 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.63 | 294 | Well volume: 30.0 uL Well Ingredients: Salt: 0.2571428571 M (1.9285714282 uL of stock 4.0 M) potassium formate Precipitant: 20.0 %w/v (12.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 0.1 M (3.0 uL of stock 1.0 M) Tris (pH 7.63) Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.1 uL Drop protein volume: 0.3 uL Protein: 6.00 mg/mL (0.17 mM) Compound1: small molecule to aid crystallization (1.20 mM) Soak of 10mM compound 3 for > 1h into co-crystals of TrkA + compound1 |