☰ Navigation Tabs
Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with SORAFENIB (BAY 43-9006)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AG8 PDB ENTRY 4AG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 286 CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C USING PRECIPITANT SOLUTIONS CONTAINING APPROXIMATELY: 0.2M SODIUM CITRATE AND 14-21% (W/V) POLYETHYLENE GLYCOL 3350., pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.818 α = 90 b = 56.479 β = 95.42 c = 52.052 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 81 IMAGE PLATE MARRESEARCH MIRRORS 2007-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU2000
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 2.02 50 92.2 0.04 38 3.7 23908 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 2.02 2.09 43.6 0.13 6 1.9
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 4AG8 2.03 15 22631 1218 94 0.17831 0.17547 0.1763 0.23022 0.2272 RANDOM 29.658
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] 0.84 -0.37 -0.44 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 21.002 r_dihedral_angle_3_deg 17.192 r_dihedral_angle_1_deg 5.747 r_scangle_it 3.102 r_scbond_it 2.003 r_mcangle_it 1.365 r_angle_refined_deg 1.303 r_mcbond_it 0.799 r_angle_other_deg 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 21.002 r_dihedral_angle_3_deg 17.192 r_dihedral_angle_1_deg 5.747 r_scangle_it 3.102 r_scbond_it 2.003 r_mcangle_it 1.365 r_angle_refined_deg 1.303 r_mcbond_it 0.799 r_angle_other_deg 0.694 r_nbd_other 0.375 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.238 r_nbtor_other 0.225 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.185 r_mcbond_other 0.161 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 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 2453 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CCP4 phasing