3VID

Crystal structure of human VEGFR2 kinase domain with Compound A.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52771.3M TRI-SODIUM CITRATE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1542.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.24α = 90
b = 94.62β = 90
c = 96.37γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2004-10-14
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.367.521575411

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.367.521493279797.060.247150.245350.28135RANDOM47.94
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]
0.160.78-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.535
r_dihedral_angle_3_deg15.305
r_dihedral_angle_4_deg11.693
r_dihedral_angle_1_deg6.104
r_scangle_it1.591
r_angle_refined_deg1.238
r_scbond_it0.981
r_angle_other_deg0.846
r_mcangle_it0.779
r_mcbond_it0.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.535
r_dihedral_angle_3_deg15.305
r_dihedral_angle_4_deg11.693
r_dihedral_angle_1_deg6.104
r_scangle_it1.591
r_angle_refined_deg1.238
r_scbond_it0.981
r_angle_other_deg0.846
r_mcangle_it0.779
r_mcbond_it0.414
r_chiral_restr0.068
r_mcbond_other0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2406
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms17

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling