5YP2
Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-1A |
Synchrotron site | Photon Factory |
Beamline | BL-1A |
Temperature [K] | 95 |
Detector technology | PIXEL |
Collection date | 2012-06-23 |
Detector | DECTRIS PILATUS 2M |
Wavelength(s) | 1.100 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 59.880, 120.220, 231.890 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 40.000 - 2.130 |
R-factor | 0.18028 |
Rwork | 0.178 |
R-free | 0.22627 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5yp1 |
RMSD bond length | 0.017 |
RMSD bond angle | 1.864 |
Data reduction software | xia2 (0.5.170) |
Data scaling software | XSCALE |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.050 | 2.170 |
High resolution limit [Å] | 2.130 | 2.130 |
Rmerge | 0.140 | 0.876 |
Rmeas | 0.154 | 0.972 |
Rpim | 0.063 | 0.413 |
Number of reflections | 93976 | 4211 |
<I/σ(I)> | 9 | 2 |
Completeness [%] | 99.3 | 90.8 |
Redundancy | 5.8 | 5.3 |
CC(1/2) | 0.994 | 0.610 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293.15 | 12% PEG 20000, 100mM MES pH6.5, 20% Glycerol, 1.5mM inhibitor 1c |