3CJF | pdb_00003cjf

Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VR2	Unliganded Vegfr2 kinase domain solved in house - similar to pdb entry 1VR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.435	α = 90
b = 94.742	β = 90
c = 96.797	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2000-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

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	40	96.3	0.042	42.4	6.6	18647	18596	-3		43.5

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	74.3		0.423	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Unliganded Vegfr2 kinase domain solved in house - similar to pdb entry 1VR2	2.15	34.92	17994	601	96.16	0.20518	0.20352	0.21	0.25813	0.27	RANDOM	62.689

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]
2.38			0.72		-3.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.311
r_dihedral_angle_1_deg	22.538
r_dihedral_angle_4_deg	18.243
r_dihedral_angle_3_deg	17.224
r_scangle_it	2.072
r_scbond_it	1.393
r_angle_refined_deg	1.309
r_mcangle_it	1.002
r_angle_other_deg	0.896
r_mcbond_it	0.634
r_symmetry_hbond_refined	0.227
r_nbd_refined	0.225
r_nbd_other	0.191
r_nbtor_refined	0.179
r_symmetry_vdw_refined	0.172
r_symmetry_vdw_other	0.157
r_xyhbond_nbd_refined	0.15
r_mcbond_other	0.127
r_nbtor_other	0.086
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2229
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing