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Crystal structure of MerTK kinase domain in complex with LDC1267
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 7.5 293 0.05M Tris pH 7.5, 4.4M NaCl
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.725 α = 90 b = 92.787 β = 90 c = 70.994 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 2016-07-22 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 1.762 65.588 89.1 0.038 0.042 0.016 1 19 6 23363
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 1.762 1.893 42.9 0.717 0.811 0.367 0.702 4
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 1.762 65.588 22170 1145 75.71 0.2016 0.1992 0.2075 0.2532 0.2006 RANDOM 47.515
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] -0.01 0.43 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.554 r_dihedral_angle_3_deg 14.248 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_1_deg 5.636 r_angle_refined_deg 1.502 r_angle_other_deg 0.997 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.554 r_dihedral_angle_3_deg 14.248 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_1_deg 5.636 r_angle_refined_deg 1.502 r_angle_other_deg 0.997 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2148 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction Aimless data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction