☰ Navigation Tabs
KDR in complex with ligand lenvatinib
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 277 0.1M CHES,5-20% PEG 8000, pH 9.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.334 α = 90 b = 84.225 β = 100.2 c = 46.892 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 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 1.57 46.15 99.5 0.06 4.2 44907
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 1.57 1.82 99.7 0.444 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.57 46.15 40823 4082 99.52 0.18372 0.18089 0.21188 0.2452 RANDOM 29.321
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] 0.11 -1.17 -0.51 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_3_deg 11.547 r_dihedral_angle_1_deg 5.942 r_scbond_it 4.204 r_mcangle_it 3.31 r_mcbond_it 2.584 r_mcbond_other 2.583 r_angle_refined_deg 1.58 r_angle_other_deg 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_3_deg 11.547 r_dihedral_angle_1_deg 5.942 r_scbond_it 4.204 r_mcangle_it 3.31 r_mcbond_it 2.584 r_mcbond_other 2.583 r_angle_refined_deg 1.58 r_angle_other_deg 1.027 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 2224 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling