5YP3
Crystal structure of dipeptidyl peptidase IV (DPP IV) with Ile-Pro from Pseudoxanthomonas mexicana
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-17A |
Synchrotron site | Photon Factory |
Beamline | BL-17A |
Temperature [K] | 95 |
Detector technology | CCD |
Collection date | 2012-12-20 |
Detector | ADSC QUANTUM 270 |
Wavelength(s) | 0.9788 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 119.880, 120.120, 262.530 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 40.000 - 2.440 |
R-factor | 0.24066 |
Rwork | 0.238 |
R-free | 0.28627 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5yp1 |
RMSD bond length | 0.014 |
RMSD bond angle | 1.772 |
Data reduction software | xia2 (0.5.436) |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 60.060 | 2.470 |
High resolution limit [Å] | 2.430 | 2.430 |
Rmerge | 0.087 | 0.432 |
Rmeas | 0.094 | 0.515 |
Rpim | 0.034 | 0.271 |
Number of reflections | 139194 | 5737 |
<I/σ(I)> | 14.3 | 2 |
Completeness [%] | 97.3 | 81.2 |
Redundancy | 6.7 | 3.3 |
CC(1/2) | 0.998 | 0.787 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293.15 | 12% PEG 20000, 0.1M MES pH6.5, 20% Glycerol, 5.5mM DiprotinA(IPI) |