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Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100mM HEPES, 880-1440mM tri-sodium citrate, pH 7.0-8.0, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.719 α = 90 b = 56.354 β = 95.61 c = 51.875 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 RIGAKU JUPITER 210 2007-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0 SPring-8 BL32B2
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 2.49 67.57 98.9 0.069 11.4 3.73 13639
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 2.49 2.58 93.7 0.377 3.1 3.68 1288
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 2.49 37.35 13619 681 98.75 0.2096 0.2068 0.2214 0.2621 0.268 RANDOM 73.172
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] 1.27 -0.7 -2.14 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 14.122 r_dihedral_angle_3_deg 13.891 r_scangle_it 6.677 r_dihedral_angle_1_deg 4.922 r_scbond_it 4.759 r_mcangle_it 3.123 r_mcbond_it 1.9 r_angle_refined_deg 0.923 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 14.122 r_dihedral_angle_3_deg 13.891 r_scangle_it 6.677 r_dihedral_angle_1_deg 4.922 r_scbond_it 4.759 r_mcangle_it 3.123 r_mcbond_it 1.9 r_angle_refined_deg 0.923 r_nbtor_refined 0.298 r_nbd_refined 0.166 r_symmetry_hbond_refined 0.156 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2395 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 26
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling