3U6J

Crystal structure of the VEGFR2 kinase domain in complex with a pyrazolone inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	17% PEG 5000 monomethyl ether, 75 mM ammonium sulfate, 25 mM sodium chloride, 100 mM HEPES, 8% isopropanol, 40 mM beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.194	α = 90
b = 65.268	β = 117.94
c = 57.323	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	IMAGE PLATE	RIGAKU RAXIS IV++		2007-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	2.15	50	99	0.105	9.6	3.1		19876		-3

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	2.15	2.23	97.6		0.471		2.6	1947

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		THROUGHOUT	2.15	50	19863	1449	99.02	0.1956	0.1928	0.2303	RANDOM	34.3479

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]
1.51		1.02	-0.71		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.707
r_dihedral_angle_4_deg	16.038
r_dihedral_angle_3_deg	12.512
r_dihedral_angle_1_deg	5.204
r_scangle_it	1.614
r_angle_refined_deg	1.074
r_mcangle_it	1.023
r_scbond_it	0.981
r_mcbond_it	0.603
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.707
r_dihedral_angle_4_deg	16.038
r_dihedral_angle_3_deg	12.512
r_dihedral_angle_1_deg	5.204
r_scangle_it	1.614
r_angle_refined_deg	1.074
r_mcangle_it	1.023
r_scbond_it	0.981
r_mcbond_it	0.603
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.179
r_nbd_refined	0.164
r_symmetry_hbond_refined	0.118
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2484
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	39

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
EPMR	phasing

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.