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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 2.42 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 0.2121 0.25813 0.2669 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
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