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KDR in complex with ligand sorafenib
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 10-25% PEG 3350, Na3Citrate, 0.1M Bis-Tris propane, pH 8.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.97 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.921 α = 90 b = 57.357 β = 94.17 c = 52.17 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 100 PIXEL PSI PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99985 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 1.9 67.78 95.9 0.031 2.7 30435
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 1.9 2.15 97.6 0.448 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.9 67.78 28257 2178 95.92 0.18771 0.18479 0.1931 0.22406 0.2301 RANDOM 48.93
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] 0.67 -1.23 -0.33 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.093 r_dihedral_angle_4_deg 21.858 r_dihedral_angle_3_deg 12.978 r_scbond_it 6.632 r_mcangle_it 6.243 r_dihedral_angle_1_deg 6.143 r_mcbond_it 5.164 r_mcbond_other 5.142 r_angle_refined_deg 1.469 r_angle_other_deg 0.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.093 r_dihedral_angle_4_deg 21.858 r_dihedral_angle_3_deg 12.978 r_scbond_it 6.632 r_mcangle_it 6.243 r_dihedral_angle_1_deg 6.143 r_mcbond_it 5.164 r_mcbond_other 5.142 r_angle_refined_deg 1.469 r_angle_other_deg 0.999 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 2402 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling