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Crystal structure of Cyclin-G associated kinase (GAK) complexed with selective 12i inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293.15 9% Broad-molecular weight PEG Smears (BMW PEG smears), 0.1M MES pH 6.2, 0.15M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.01 38.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.706 α = 109.7 b = 68.703 β = 95.08 c = 89.868 γ = 99.04
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 PILATUS 2M 2013-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
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 2.1 43.58 94.7 0.071 11.9 3.7 45797
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 2.1 2.21 92.4 0.602 2 3.6
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 4C58 2.1 43.58 43487 2310 94.74 0.19432 0.19234 0.2173 0.23154 0.2493 RANDOM 70.498
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] 2.6 0.31 -0.64 0.5 -0.55 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_4_deg 18.635 r_dihedral_angle_3_deg 14.354 r_long_range_B_refined 7.26 r_long_range_B_other 7.259 r_dihedral_angle_1_deg 6.853 r_scangle_other 2.617 r_mcangle_it 2.231 r_mcangle_other 2.231 r_scbond_it 1.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_4_deg 18.635 r_dihedral_angle_3_deg 14.354 r_long_range_B_refined 7.26 r_long_range_B_other 7.259 r_dihedral_angle_1_deg 6.853 r_scangle_other 2.617 r_mcangle_it 2.231 r_mcangle_other 2.231 r_scbond_it 1.645 r_scbond_other 1.642 r_angle_refined_deg 1.436 r_mcbond_it 1.305 r_mcbond_other 1.305 r_angle_other_deg 0.89 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5909 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing