3CJG

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VR2Unliganded Vegfr2 kinase domain solved in house - similar to pdb entry 1VR2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPVAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4650.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.7α = 90
b = 95.54β = 90
c = 97.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2000-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.254099.30.046406.91712516998-340.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.33950.4012.76

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUnliganded Vegfr2 kinase domain solved in house - similar to pdb entry 1VR22.2519.951653454499.080.208750.207330.25316RANDOM47.869
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]
2.98-2.77-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.536
r_dihedral_angle_1_deg18.458
r_dihedral_angle_4_deg17.807
r_dihedral_angle_3_deg14.87
r_scangle_it2.049
r_scbond_it1.398
r_angle_refined_deg1.277
r_mcangle_it1.06
r_angle_other_deg0.868
r_mcbond_it0.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.536
r_dihedral_angle_1_deg18.458
r_dihedral_angle_4_deg17.807
r_dihedral_angle_3_deg14.87
r_scangle_it2.049
r_scbond_it1.398
r_angle_refined_deg1.277
r_mcangle_it1.06
r_angle_other_deg0.868
r_mcbond_it0.615
r_nbd_refined0.208
r_symmetry_vdw_other0.191
r_nbd_other0.188
r_symmetry_hbond_refined0.18
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.132
r_mcbond_other0.111
r_nbtor_other0.085
r_chiral_restr0.073
r_symmetry_vdw_refined0.066
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2249
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing