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Crystal structure of human VEGFR2 kinase domain with Compound A.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 1.3M TRI-SODIUM CITRATE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.24 α = 90 b = 94.62 β = 90 c = 96.37 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2004-10-14
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 67.52 15754 1 1
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 2.3 67.52 14932 797 97.06 0.24715 0.24535 0.2455 0.28135 0.2866 RANDOM 47.94
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 0.78 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.535 r_dihedral_angle_3_deg 15.305 r_dihedral_angle_4_deg 11.693 r_dihedral_angle_1_deg 6.104 r_scangle_it 1.591 r_angle_refined_deg 1.238 r_scbond_it 0.981 r_angle_other_deg 0.846 r_mcangle_it 0.779 r_mcbond_it 0.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.535 r_dihedral_angle_3_deg 15.305 r_dihedral_angle_4_deg 11.693 r_dihedral_angle_1_deg 6.104 r_scangle_it 1.591 r_angle_refined_deg 1.238 r_scbond_it 0.981 r_angle_other_deg 0.846 r_mcangle_it 0.779 r_mcbond_it 0.414 r_chiral_restr 0.068 r_mcbond_other 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2406 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 17
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling