7G5F
Crystal Structure of rat Autotaxin in complex with 1H-benzotriazol-5-yl-[rac-(1R,2R,6S,7S)-9-[4-(cyclopropylmethoxy)naphthalene-2-carbonyl]-4,9-diazatricyclo[5.3.0.02,6]decan-4-yl]methanone, i.e. SMILES N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)c1ccc2c(c1)N=NN2)C(=O)c1cc(c2c(c1)cccc2)OCC1CC1 with IC50=0.00985223 microM
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SLS BEAMLINE X10SA |
Synchrotron site | SLS |
Beamline | X10SA |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2012-10-28 |
Detector | PSI PILATUS 6M |
Wavelength(s) | 0.99986 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 84.078, 91.953, 120.100 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 45.980 - 2.300 |
R-factor | 0.2182 |
Rwork | 0.215 |
R-free | 0.26990 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | inhouse model |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 45.980 | 45.980 | 2.360 |
High resolution limit [Å] | 2.300 | 10.290 | 2.300 |
Rmerge | 0.195 | 0.048 | 1.625 |
Rmeas | 0.215 | 0.053 | 1.788 |
Total number of observations | 247830 | ||
Number of reflections | 41902 | 550 | 3055 |
<I/σ(I)> | 7.14 | 20.03 | 1.38 |
Completeness [%] | 99.4 | 98.4 | 99.3 |
Redundancy | 5.915 | 5.947 | 5.792 |
CC(1/2) | 0.992 | 0.998 | 0.730 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 293 | 15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL |