6D3O

Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with HH4, an alpha/beta-Peptide with Irregular Secondary Structure

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.649	α = 90
b = 101.649	β = 90
c = 59.988	γ = 120

Symmetry
Space Group	P 63

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 300 mm CCD		2017-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3	50	100	0.149	0.156	0.047	0.997	13	11.1		7198			66.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.18	100		1.43	1.5	0.443	0.67	1.7	11.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VPF	3.1	33.29	6255	279	99.94	0.2192	0.2166	0.2789	RANDOM	77.405

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]
-1.06	-0.53		-1.06		3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.537
r_dihedral_angle_4_deg	22.188
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_1_deg	6.194
r_angle_refined_deg	1.353
r_angle_other_deg	1.065
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.537
r_dihedral_angle_4_deg	22.188
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_1_deg	6.194
r_angle_refined_deg	1.353
r_angle_other_deg	1.065
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1712
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	8

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.