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Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine
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 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.7 α = 90 b = 95.54 β = 90 c = 97.01 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 1.00 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 2.25 40 99.3 0.046 40 6.9 17125 16998 -3 40.6
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 2.25 2.33 95 0.401 2.76
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 2.25 19.95 16534 544 99.08 0.20875 0.20733 0.2134 0.25316 0.2591 RANDOM 47.869
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.536 r_dihedral_angle_1_deg 18.458 r_dihedral_angle_4_deg 17.807 r_dihedral_angle_3_deg 14.87 r_scangle_it 2.049 r_scbond_it 1.398 r_angle_refined_deg 1.277 r_mcangle_it 1.06 r_angle_other_deg 0.868 r_mcbond_it 0.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.536 r_dihedral_angle_1_deg 18.458 r_dihedral_angle_4_deg 17.807 r_dihedral_angle_3_deg 14.87 r_scangle_it 2.049 r_scbond_it 1.398 r_angle_refined_deg 1.277 r_mcangle_it 1.06 r_angle_other_deg 0.868 r_mcbond_it 0.615 r_nbd_refined 0.208 r_symmetry_vdw_other 0.191 r_nbd_other 0.188 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.132 r_mcbond_other 0.111 r_nbtor_other 0.085 r_chiral_restr 0.073 r_symmetry_vdw_refined 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 2249 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing