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Crystal structure of pseudokinase CASK in complex with compound 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.355 α = 76.2 b = 66.844 β = 89.99 c = 130.203 γ = 90
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 DECTRIS EIGER2 X 16M 2018-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99986 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.93 42.15 91.6 0.061 0.085 0.043 0.996 9.9 3.9 93376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2 90.6 0.492 0.706 0.357 0.831 2 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3C0I 1.93 42.15 88899 4466 91.58 0.196 0.1946 0.2238 0.2578 RANDOM 34.554
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] 8.97 0.47 0.33 -18.56 0.72 9.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.844 r_dihedral_angle_4_deg 21.631 r_dihedral_angle_3_deg 14.299 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.291 r_angle_other_deg 0.902 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.844 r_dihedral_angle_4_deg 21.631 r_dihedral_angle_3_deg 14.299 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.291 r_angle_other_deg 0.902 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9497 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 224
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing