3VHK

Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	100mM HEPES, 880-1440mM tri-sodium citrate, pH 7.0-8.0, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.719	α = 90
b = 56.354	β = 95.61
c = 51.875	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU JUPITER 210		2007-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.0	SPring-8	BL32B2

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	2.49	67.57	98.9	0.069	11.4	3.73		13639

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	2.49	2.58	93.7		0.377	3.1	3.68	1288

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.49	37.35	13619	681	98.75	0.2096	0.2068	0.2621	RANDOM	73.172

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]
1.27		-0.7	-2.14		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.821
r_dihedral_angle_4_deg	14.122
r_dihedral_angle_3_deg	13.891
r_scangle_it	6.677
r_dihedral_angle_1_deg	4.922
r_scbond_it	4.759
r_mcangle_it	3.123
r_mcbond_it	1.9
r_angle_refined_deg	0.923
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.821
r_dihedral_angle_4_deg	14.122
r_dihedral_angle_3_deg	13.891
r_scangle_it	6.677
r_dihedral_angle_1_deg	4.922
r_scbond_it	4.759
r_mcangle_it	3.123
r_mcbond_it	1.9
r_angle_refined_deg	0.923
r_nbtor_refined	0.298
r_nbd_refined	0.166
r_symmetry_hbond_refined	0.156
r_symmetry_vdw_refined	0.136
r_xyhbond_nbd_refined	0.093
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2395
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	26

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.