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Crystal structure of the VEGFR2 kinase domain in complex with a bisamide inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol
, pH 8.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.919 α = 90 b = 67.552 β = 92.524 c = 88.73 γ = 90
Symmetry Space Group P 1 21 1
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-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 2.7 30 99.9 0.126 12.4 5.6 18034 18016 -3
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) 2.7 2.8 99.5 0.488 2.8 5 1779
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.7 30 18003 1409 99.7 0.224 0.219 0.2184 0.286 0.2796 RANDOM 31.54
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] -1.23 0.31 -0.96 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.142 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_3_deg 15.027 r_dihedral_angle_1_deg 5.107 r_mcangle_it 1.007 r_angle_refined_deg 0.952 r_scangle_it 0.882 r_mcbond_it 0.565 r_scbond_it 0.546 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.142 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_3_deg 15.027 r_dihedral_angle_1_deg 5.107 r_mcangle_it 1.007 r_angle_refined_deg 0.952 r_scangle_it 0.882 r_mcbond_it 0.565 r_scbond_it 0.546 r_nbtor_refined 0.298 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4429 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 54
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction