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MerTK kinase domain with type 1.5 inhibitor containing a di-methyl pyrazole group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Tris pH 8.5, 4.3 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.71 α = 90 b = 94.172 β = 90 c = 71.627 γ = 90
Symmetry Space Group C 2 2 21
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 6M 2017-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.89 66.07 94.6 0.071 0.078 0.031 0.999 15.3 6.4 16521
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 1.895 2.027 67.6 1.234 1.356 0.554 0.552 5.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BRB 1.89 66.07 15714 805 65.38 0.2215 0.2187 0.2198 0.2819 0.2924 RANDOM 47.483
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] 0.35 -0.17 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.904 r_dihedral_angle_4_deg 13.858 r_dihedral_angle_3_deg 12.551 r_dihedral_angle_1_deg 4.977 r_angle_refined_deg 1.051 r_angle_other_deg 0.862 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.904 r_dihedral_angle_4_deg 13.858 r_dihedral_angle_3_deg 12.551 r_dihedral_angle_1_deg 4.977 r_angle_refined_deg 1.051 r_angle_other_deg 0.862 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2145 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 39
Software Software Software Name Purpose autoPROC data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing