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Structure of VEGFR2 kinase domain in complex with BIBF1120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 0.1M HEPES, 2.1M Ammonium Sulphate, 3% PEG MME 550, 10mM Beta-Mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.25 α = 90 b = 94.44 β = 90 c = 96.22 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 CCD MARMOSAIC 225 mm CCD 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9799 SLS X06SA
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 30 98.4 0.087 9.91 23933 -3 32.839
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 2.1 91.2 0.559 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1VR2 2.1 28.54 19934 19934 1050 100 0.221 0.217 0.2183 0.279 0.2847 RANDOM 24.366
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] -0.87 2.84 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_4_deg 17.038 r_dihedral_angle_3_deg 16.389 r_dihedral_angle_1_deg 8.311 r_scangle_it 2.529 r_scbond_it 1.789 r_angle_refined_deg 1.633 r_mcangle_it 1.354 r_mcbond_it 1.184 r_angle_other_deg 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_4_deg 17.038 r_dihedral_angle_3_deg 16.389 r_dihedral_angle_1_deg 8.311 r_scangle_it 2.529 r_scbond_it 1.789 r_angle_refined_deg 1.633 r_mcangle_it 1.354 r_mcbond_it 1.184 r_angle_other_deg 0.997 r_symmetry_hbond_refined 0.267 r_symmetry_vdw_other 0.22 r_nbd_refined 0.206 r_nbd_other 0.2 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.181 r_mcbond_other 0.155 r_chiral_restr 0.114 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2362 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 65
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction