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Src Kinase Domain in complex with ponatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris 20 mM pH 8, 150 mM Sodium chloride, 1 mM DTT, 2-propanol and PEG 4.000
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.153 α = 90 b = 124.631 β = 90.15 c = 63.591 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 80 PIXEL DECTRIS PILATUS 6M 2019-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.49 63.59 85.2 0.18 0.225 0.924 5.1 2.5 21420
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 2.49 8.94 0.041
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 3EL8 2.49 63.59 20255 1164 93.59 0.1793 0.1751 0.1876 0.2521 0.2534 RANDOM 43.689
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] -14.52 1.34 48.63 -34.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.773 r_dihedral_angle_3_deg 17.593 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_1_deg 7.143 r_angle_refined_deg 1.757 r_angle_other_deg 1.036 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.773 r_dihedral_angle_3_deg 17.593 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_1_deg 7.143 r_angle_refined_deg 1.757 r_angle_other_deg 1.036 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4160 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction