6T9D

Crystal structure of a bispecific DutaFab in complex with human VEGF121

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	VEGFA-121 from Peprotech, catalogue number 100-20A, was mixed at a 1:1 molar ratio to VEGF monomer. The complex was concentrated to 11 mg/ml. Crystallization involved hanging drop vapour diffusion against 0.1 M MES pH 6.5 and 1.6 M magnesium sulphate. Crystals grew in about 120 days and were frozen in liquid nitrogen with 20 % glycerol as cryoprotectant.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.08	α = 90
b = 107.875	β = 95.34
c = 87.369	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	KB MIRRORS	2014-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.9	30	98.9	0.212	6.7	3		28318			37.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.1	98.2		0.842	1.5	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1BJ1, 1JPS	2.905	29.294	28317	1416	98.879	0.216	0.2124	0.2801	35.023

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.396		-0.886	0.703		0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.368
r_dihedral_angle_1_deg	21.628
r_dihedral_angle_3_deg	18.883
r_dihedral_angle_4_deg	17.518
r_lrange_it	6.612
r_lrange_other	6.61
r_mcangle_it	3.925
r_mcangle_other	3.925
r_scangle_it	3.615
r_scangle_other	3.615
r_mcbond_it	2.372
r_mcbond_other	2.372
r_scbond_it	2.192
r_scbond_other	2.192
r_angle_refined_deg	1.525
r_angle_other_deg	1.169
r_symmetry_nbd_refined	0.327
r_nbd_other	0.248
r_nbd_refined	0.185
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.168
r_ncsr_local_group_3	0.086
r_ncsr_local_group_1	0.081
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_2	0.068
r_chiral_restr	0.055
r_symmetry_xyhbond_nbd_refined	0.043
r_symmetry_xyhbond_nbd_other	0.014
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8047
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing