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Crystal Structure of the Kinase domain of Human VEGFR2 with imidazo[1,2-b]pyridazine derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M trisHCl pH 8.5, 1.2M tri-sodium citrate, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.093 α = 90 b = 55.77 β = 94.41 c = 51.572 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 100 CCD ADSC QUANTUM 210r 2006-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
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 1.52 50 96.3 0.042 17.9 3.8 56337 19.987
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 1.52 1.57 76.9 0.434 2.3 4468
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 (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 1.52 39.32 56331 2867 96.26 0.1619 0.1609 0.163 0.1821 0.1832 RANDOM 23.4135
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] 0.77 -0.65 -0.98 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.026 r_dihedral_angle_4_deg 23.153 r_dihedral_angle_3_deg 12.223 r_dihedral_angle_1_deg 5.42 r_scangle_it 3.696 r_scbond_it 2.61 r_mcangle_it 1.688 r_angle_refined_deg 1.333 r_mcbond_it 1.093 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.026 r_dihedral_angle_4_deg 23.153 r_dihedral_angle_3_deg 12.223 r_dihedral_angle_1_deg 5.42 r_scangle_it 3.696 r_scbond_it 2.61 r_mcangle_it 1.688 r_angle_refined_deg 1.333 r_mcbond_it 1.093 r_nbtor_refined 0.315 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2438 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 36
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing