3EWH | pdb_00003ewh

Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	277	PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol , pH 8.0, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.319	α = 90
b = 84.38	β = 99.33
c = 47.404	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++		2006-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.6	30	93.3	0.051	22.3	3.1		39565		-3	23.8

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)
	1.6	1.66	47.7		0.266	2.5	1.7	2012

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	21.1	42366	39541	1973	93.33	0.208	0.206	0.21	0.234	0.24	RANDOM	19.4

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]
0.15		-0.41	-0.31		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.804
r_dihedral_angle_4_deg	17.968
r_dihedral_angle_3_deg	11.65
r_dihedral_angle_1_deg	5.276
r_scangle_it	1.937
r_scbond_it	1.278
r_mcangle_it	1.244
r_angle_refined_deg	1.035
r_mcbond_it	0.799
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.804
r_dihedral_angle_4_deg	17.968
r_dihedral_angle_3_deg	11.65
r_dihedral_angle_1_deg	5.276
r_scangle_it	1.937
r_scbond_it	1.278
r_mcangle_it	1.244
r_angle_refined_deg	1.035
r_mcbond_it	0.799
r_nbtor_refined	0.305
r_nbd_refined	0.182
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.096
r_symmetry_hbond_refined	0.076
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2424
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	43

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
AMoRE	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.