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Crystal structure of MerTK kinase domain in complex with Merestinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRB pdbid 3BRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 293 0.1M MES pH 6.2, 0.75M LiCl, 23% PEG 6k
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.119 α = 90 b = 130.983 β = 90 c = 54.192 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-F 2016-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.855 46.56 93.8 0.108 0.118 0.047 0.998 10.6 6.3 19081
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 1.855 2.075 63.6 0.776 0.91 0.466 0.582 3.5
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 pdbid 3BRB 1.87 46.56 18099 960 68.59 0.1967 0.1953 0.204 0.2239 0.1991 RANDOM 36.09
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] 0.51 -0.43 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_3_deg 13.612 r_dihedral_angle_4_deg 13.263 r_dihedral_angle_1_deg 6.092 r_angle_refined_deg 1.303 r_angle_other_deg 0.94 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_3_deg 13.612 r_dihedral_angle_4_deg 13.263 r_dihedral_angle_1_deg 6.092 r_angle_refined_deg 1.303 r_angle_other_deg 0.94 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing