☰ Navigation Tabs
CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH AXITINIB (AG-013736) (N-Methyl-2-(3-((E)-2-pyridin-2-yl- vinyl)-1H-indazol-6-ylsulfanyl)-benzamide)
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 286 CRYSTALS WERE GROWN AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD USING PRECIPITANT SOLUTIONS CONTAINING: 0.2M SODIUM CITRATE (PH 6.0 -6.5) AND 14-21% (W/V) POLYETHYLENE GLYCOL MW = 3350
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.492 α = 90 b = 56.922 β = 97.12 c = 50.787 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 87 CCD ADSC QUANTUM 315 2007-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 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 2 50 97.4 0.04 35 3.3 25951 2 26.7
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 2.05 78.6 0.39 2 2
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-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 43.38 24733 710 92 0.204 0.2012 0.251 0.2493 RANDOM 46.2
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] 1.86 -0.25 -1.06 -0.8
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 3.5 c_mcangle_it 2.36 c_scbond_it 2.31 c_mcbond_it 1.51 c_angle_deg 0.8 c_improper_angle_d 0.63 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 3.5 c_mcangle_it 2.36 c_scbond_it 2.31 c_mcbond_it 1.51 c_angle_deg 0.8 c_improper_angle_d 0.63 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2442 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 28
Software Software Software Name Purpose CNX refinement HKL-2000 data reduction SCALEPACK data scaling EPMR phasing