3NOX
Crystal structure of human DPP-IV in complex with Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS BEAMLINE X29A |
Synchrotron site | NSLS |
Beamline | X29A |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2006-03-11 |
Detector | ADSC Q315 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 65.451, 67.072, 420.443 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 35.624 - 2.338 |
R-factor | 0.1977 |
Rwork | 0.196 |
R-free | 0.26400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3bjm |
RMSD bond length | 0.008 |
RMSD bond angle | 1.158 |
Data reduction software | HKL-2000 ((DENZO)) |
Data scaling software | HKL-2000 ((SCALEPACK)) |
Phasing software | AMoRE |
Refinement software | PHENIX ((PHENIX.REFINE: DEV_446)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.430 |
High resolution limit [Å] | 2.350 | 2.350 |
Rmerge | 0.113 | |
Number of reflections | 68839 | |
<I/σ(I)> | 14 | 2.6 |
Completeness [%] | 86.5 | 50.9 |
Redundancy | 6.8 | 3.6 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | CRYSTALS GROWN FROM 2 UL EQUIVOLUME MIXTURE OF PROTEIN SOLUTION (0.1 M NACL, 20 MM TRIS-HCL BUFFER PH 7.8, 9.8 MG/ML PROTEIN) AND CRYSTALLIZATION SOLUTION (17% W/V PEG 3350, 15% W/V GLYCEROL, 200 MM MGCL2, 100 MM TRIS-HCL BUFFER PH 8.5). SUFFICIENT 100 MM LIGAND STOCK SOLUTION (NEAT DMSO) ADDED TO ACHIEVE 1 MM LIGAND CONCENTRATION. SOAKED OVERNIGHT. HARVESTED DIRECTLY AND CRYO-PRESERVED IN LN2., VAPOR DIFFUSION, HANGING DROP, temperature 298K |