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CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN 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 1VR2 PDB ENTRY 1VR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 CRYSTALS WERE GROWN AT 4 OR 13 C BY THE HANGING DROP VAPOR DIFFUSION BY MIXING 2 MICORLITERS OF PROTEIN-INHIBITOR COMPLEX SOLUTION WITH 2 MICROLITERS OF MOTHER LIQUOR (100 MM HEPES (PH 7.5), 200 MM AMMONIUM SULFATE, 5% (V/V) MPD, AND 15-20% (W/V) POLYETHYLENE GLYCOL (MW = 6000)). BEFORE SEALING THE COVERSLIPS ABOVE THE RESERVOIRS, BETA-MERCAPTOETHANOL WAS ADDED TO THE RESERVOIRS TO A FINAL CONCENTRATION OF 60 MM. THIS PROCEDURE PRODUCED MICROCRYSTALS THAT WERE SUBSEQUENTLY USED TO SEED MORE CRYSTALLIZATION DROPS AFTER 12-18 HOURS OF EQUILIBRATION.
Crystal Properties Matthews coefficient Solvent content 2.87 57.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.66 α = 90 b = 57.221 β = 93.44 c = 51.829 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 IMAGE PLATE MARRESEARCH MIRRORS 1999-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.95 20 99 0.05 23 2.7 28556 2
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 1.95 2.02 97.7 0.18 7.7
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 1VR2 1.95 19.84 27105 1450 98.75 0.19726 0.19493 0.1968 0.2415 0.2391 RANDOM 25.15
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] 0.21 -0.34 0.03 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.439 r_scangle_it 2.818 r_scbond_it 1.671 r_mcangle_it 1.133 r_angle_refined_deg 1.104 r_mcbond_it 0.58 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.439 r_scangle_it 2.818 r_scbond_it 1.671 r_mcangle_it 1.133 r_angle_refined_deg 1.104 r_mcbond_it 0.58 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other 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_mcbond_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 2381 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing