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Crystal structure of the VEGFR2 kinase domain in complex with PF- 00337210 (N,2-dimethyl-6-(7-(2-morpholinoethoxy)quinolin-4-yloxy) benzofuran-3-carboxamide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VR2 PDB ENTRY 1VR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 286 PROTEIN PRODUCTION, PROTEIN PURIFICATION, AND COCRYSTALLIZATION WERE PERFORMED AS PREVIOUSLY DESCRIBED (PUBLISHED INTERNATIONAL PATENT APPLICATION WO 2004/092217 HANGING DROP VAPOR DIFFUSION AT 13 DEGREES C. 2 MICROLITERS OF A 7.7 MG/ML PROTEIN SOLUTION (IN 50 MM HEPES 7.5, 30 MM SODIUM CHLORIDE, 5 MM DTT, AND 5% DMSO) WAS MIXED WITH 2 MICROLITERS OF CRYSTALLIZATION SOLUTION (100 MM HEPES PH 7.5, 20% PEG 6K AND 5% MPD) AND SUSPENDED OVER 1 ML OF CRYSTALLIZATION SOLUTION PLUS 5 MICROLITERS BME.
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.267 α = 90 b = 56.827 β = 94.18 c = 52.187 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 89 CCD ADSC CCD 2004-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 1.45 50 95.8 0.06 22 4.4 67226 1
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 1.45 1.5 68.2 0.48 1.22 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 PDB ENTRY 1VR2 1.5 19.92 59334 3178 98.83 0.21852 0.21747 0.2157 0.23808 0.2349 RANDOM 23.671
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] 0.16 -0.63 -0.41 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_angle_other_deg 16.781 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_3_deg 13.856 r_dihedral_angle_1_deg 4.921 r_scangle_it 1.636 r_angle_refined_deg 1.091 r_scbond_it 1.017 r_mcangle_it 0.77 r_mcbond_it 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_angle_other_deg 16.781 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_3_deg 13.856 r_dihedral_angle_1_deg 4.921 r_scangle_it 1.636 r_angle_refined_deg 1.091 r_scbond_it 1.017 r_mcangle_it 0.77 r_mcbond_it 0.449 r_nbtor_refined 0.304 r_nbd_other 0.287 r_nbtor_other 0.214 r_nbd_refined 0.171 r_symmetry_vdw_refined 0.137 r_symmetry_hbond_refined 0.103 r_xyhbond_nbd_refined 0.092 r_chiral_restr 0.074 r_mcbond_other 0.02 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2338 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing