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Crystal Structure of the Kinase domain of Human VEGFR2 with a [1,3]thiazolo[5,4-b]pyridine derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM HEPES, 880-1440mM tri-sodium citrate, pH 7.0-8.0, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.615 α = 90 b = 56.618 β = 94.88 c = 51.819 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 315r 2010-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.992 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 1.64 50 97.2 0.052 15.4 4.1 46806
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 1.64 1.67 95.6 0.786 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.64 37.33 46773 44402 2371 97.07 0.15346 0.15147 0.19203 0.2152 RANDOM 29.926
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] 1.91 0.22 -0.52 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 20.19 r_dihedral_angle_3_deg 12.341 r_scangle_it 9.314 r_scbond_it 6.597 r_dihedral_angle_1_deg 5.302 r_mcangle_it 3.871 r_mcbond_it 2.628 r_angle_refined_deg 1.172 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 20.19 r_dihedral_angle_3_deg 12.341 r_scangle_it 9.314 r_scbond_it 6.597 r_dihedral_angle_1_deg 5.302 r_mcangle_it 3.871 r_mcbond_it 2.628 r_angle_refined_deg 1.172 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2422 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 50
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction