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MerTK kinase domain with type 1.5 inhibitor containing a di-methyl, cyano 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 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.379 α = 90 b = 92.541 β = 90 c = 71.387 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 EIGER X 9M 2017-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980073 SOLEIL PROXIMA 2
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 2.13 65.02 92.3 0.054 0.059 0.023 0.999 15.8 6.1 11729
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 2.146 2.337 56.6 0.65 0.77 0.405 0.677 3.3
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 2.13 65.02 11156 586 67.98 0.2099 0.2078 0.2089 0.2473 0.2434 RANDOM 61.622
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] 0.63 0.04 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.128 r_dihedral_angle_4_deg 22.028 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_1_deg 5.389 r_angle_refined_deg 1.145 r_angle_other_deg 0.871 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.128 r_dihedral_angle_4_deg 22.028 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_1_deg 5.389 r_angle_refined_deg 1.145 r_angle_other_deg 0.871 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2137 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 41
Software Software Software Name Purpose autoPROC data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing