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Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y6A pdb entry 1Y6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.953 α = 90 b = 95.595 β = 90 c = 95.803 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 MARRESEARCH 2001-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.7 50 94.7 0.047 31.38 6.43 37357 -3 -3 25.2
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 1.7 1.76 71.8 0.383 2.63 4.3 2767
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1Y6A 1.71 47.89 -3 35577 1139 95.19 0.20564 0.20488 0.2156 0.23005 0.2391 RANDOM 32.124
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] 0.12 1.12 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.683 r_dihedral_angle_4_deg 16.288 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.922 r_scangle_it 3.067 r_scbond_it 2.214 r_angle_refined_deg 1.485 r_mcangle_it 1.365 r_mcbond_it 1.213 r_angle_other_deg 0.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.683 r_dihedral_angle_4_deg 16.288 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.922 r_scangle_it 3.067 r_scbond_it 2.214 r_angle_refined_deg 1.485 r_mcangle_it 1.365 r_mcbond_it 1.213 r_angle_other_deg 0.823 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.219 r_mcbond_other 0.218 r_xyhbond_nbd_refined 0.21 r_symmetry_vdw_other 0.205 r_nbd_other 0.188 r_nbtor_refined 0.188 r_symmetry_hbond_refined 0.168 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2264 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing