3CJF

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
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.435α = 90
b = 94.742β = 90
c = 96.797γ = 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-ID1.000APS17-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
12.154096.30.04242.46.61864718596-343.5
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)
12.152.2374.30.4232.3

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 1VR22.1534.921799460196.160.205180.203520.25813RANDOM62.689
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]
2.380.72-3.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.311
r_dihedral_angle_1_deg22.538
r_dihedral_angle_4_deg18.243
r_dihedral_angle_3_deg17.224
r_scangle_it2.072
r_scbond_it1.393
r_angle_refined_deg1.309
r_mcangle_it1.002
r_angle_other_deg0.896
r_mcbond_it0.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.311
r_dihedral_angle_1_deg22.538
r_dihedral_angle_4_deg18.243
r_dihedral_angle_3_deg17.224
r_scangle_it2.072
r_scbond_it1.393
r_angle_refined_deg1.309
r_mcangle_it1.002
r_angle_other_deg0.896
r_mcbond_it0.634
r_symmetry_hbond_refined0.227
r_nbd_refined0.225
r_nbd_other0.191
r_nbtor_refined0.179
r_symmetry_vdw_refined0.172
r_symmetry_vdw_other0.157
r_xyhbond_nbd_refined0.15
r_mcbond_other0.127
r_nbtor_other0.086
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2229
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms50

Software

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