6T9E
Crystal structure of a bispecific DutaFab in complex with human PDGF
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-05-03 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9760 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 89.301, 75.474, 116.505 |
Unit cell angles | 90.00, 110.58, 90.00 |
Refinement procedure
Resolution | 29.735 - 2.989 |
Rwork | 0.253 |
R-free | 0.30440 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4qci |
RMSD bond length | 0.006 |
RMSD bond angle | 1.448 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0257) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 30.000 | 3.200 |
High resolution limit [Å] | 2.989 | 2.989 |
Rmerge | 0.162 | 0.773 |
Number of reflections | 29016 | 4371 |
<I/σ(I)> | 7.3 | 1.8 |
Completeness [%] | 97.7 | 92.8 |
Redundancy | 3 | 3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | DutaFab and PDGF-BB (Peprotech, catalogue number 100-13A) were mixed at a 1:1 molar ratio in relation to PDGF monomer. The complex was concentrated to 12 mg/ml and crystallization was performed by hanging drop vapour diffusion against 0.1 M Tris pH 7.5, 42 % 2-methyl-2,4-pentanediol (MPD) at 20 C. Plate-shaped crystals grew within a few weeks and were frozen in liquid nitrogen with 20% glycerol as cryo-protectant. |