4AG8

CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH AXITINIB (AG-013736) (N-Methyl-2-(3-((E)-2-pyridin-2-yl-vinyl)-1H- indazol-6-ylsulfanyl)-benzamide)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VR2	PDB ENTRY 1VR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		CRYSTALS WERE GROWN AT 4 OR 13 C BY THE HANGING DROP VAPOR DIFFUSION BY MIXING 2 MICORLITERS OF PROTEIN-INHIBITOR COMPLEX SOLUTION WITH 2 MICROLITERS OF MOTHER LIQUOR (100 MM HEPES (PH 7.5), 200 MM AMMONIUM SULFATE, 5% (V/V) MPD, AND 15-20% (W/V) POLYETHYLENE GLYCOL (MW = 6000)). BEFORE SEALING THE COVERSLIPS ABOVE THE RESERVOIRS, BETA-MERCAPTOETHANOL WAS ADDED TO THE RESERVOIRS TO A FINAL CONCENTRATION OF 60 MM. THIS PROCEDURE PRODUCED MICROCRYSTALS THAT WERE SUBSEQUENTLY USED TO SEED MORE CRYSTALLIZATION DROPS AFTER 12-18 HOURS OF EQUILIBRATION.

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.66	α = 90
b = 57.221	β = 93.44
c = 51.829	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	87	IMAGE PLATE	MARRESEARCH	MIRRORS	1999-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.95	20	99	0.05	23	2.7		28556		2

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	1.95	2.02	97.7		0.18	7.7

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	PDB ENTRY 1VR2	1.95	19.84	27105	1450	98.75	0.19726	0.19493	0.2415	RANDOM	25.15

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]
0.21		-0.34	0.03		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.439
r_scangle_it	2.818
r_scbond_it	1.671
r_mcangle_it	1.133
r_angle_refined_deg	1.104
r_mcbond_it	0.58
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2381
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing