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Structure of CHK1 8-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.4 α = 90 b = 66.57 β = 101.58 c = 55.08 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 DECTRIS PILATUS3 6M 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 1.38 33.28 96.4 0.027 0.033 0.019 0.998 18 2.7 63516
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 1.38 1.42 89.4 0.787 1.009 0.624 0.612 2.1
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 5OOT 1.4 20 58098 3013 96.64 0.1695 0.1687 0.1852 0.2018 RANDOM 32.723
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] -1.45 -0.49 0.11 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.495 r_dihedral_angle_4_deg 21.177 r_dihedral_angle_3_deg 15.434 r_dihedral_angle_1_deg 5.61 r_angle_refined_deg 2.554 r_angle_other_deg 1.19 r_chiral_restr 0.15 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.495 r_dihedral_angle_4_deg 21.177 r_dihedral_angle_3_deg 15.434 r_dihedral_angle_1_deg 5.61 r_angle_refined_deg 2.554 r_angle_other_deg 1.19 r_chiral_restr 0.15 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2106 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction