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.